Why are my faeces black in color after eating Oreos Why are my faeces black in colour the morning after I eat some Oreos?

Day 1 : Eat a handful of Oreos & the next morning your stool is black.
Day 3 : Eat a handful of cocoa flavored biscuits & the next morning your stool is normal.
Day 5 : Eat a handful of Chocolates & the next morning your stool is normal.

I'm aware of the beetroot digestion story, and how it doesn't happen to everyone. What is surprising in the case of Oreos is that it just takes a
handful of Oreos to turn the stool black. But with any other biscuits or chocolates, my faeces are normal.

I don't have anything other than anecdotal evidence but a lot (NOT ALL) of my friends have had similar experience. Just Googling "Black stool after eating Oreos" & I see a lot of people (not all) having similar experience. Do note that to my knowledge it doesn't affect my body in any way.

Why is that the case? Why doesn't it happen to everybody?
What ingredient in Oreos makes it happen? What is the physiological underpinning?
Asking this question with curiosity than caution. Looking for biological/biochemical perspective.

This is a perfectly reasonable question based on a self-adminstered (human) trial. Morever, the proposer bases their observations not on one subject but several reports. The impromptu survey of friends etc. is also acceptable. By the way, self-reported intakes/output records are an accepted method in nutrition research.

My 2-year-old child exhibited the symptoms described above, after consuming two Oreo biscuits in the afternoon. That evenings soiled nappy (diaper) revealed a dark but otherwise well-textured stool. When my concerned partner brought this to my attention, it immediately reminded me of the use of carmine red and related food dyes for the measurement of gastrointestinal transit times. The principle here is that the dyes are not absorbed in the gut, so the time from consumption to excretion gives a measure of bowel function. Short transit time means no constipation and is considered a sign of great bowel function.

Based on the observations reported for Oreos, my educated guess would be that Oreo products contain miniscule amounts of non-absorbed colorants - something that is generally regarded as safe. Self-reported symptoms are generally considered valid by health professionals. I am still intrigued by the Oreo colouring puzzle, as this colourant must be natural.


Does finite rate of increase depend on mortality of individuals in a population? As written in my lecture handouts, there two main factors in the Geometric Growth Model of populations:

$R_{0}$ is the expected lifetime reproductive output. This way, for unicellulars, for example, when time between division represents life time, if there is no mortality, $R_{0}$ is calculated as $R_{0}=1*2$, where 1 is 100% and 2 is the amount of daughter cells expected to be produced as a result of the mother cell split. We also define that for this isolated incident, $B$, the amount of births is 2, while the mother cell "dies", which leads to $D=1$.

The second factor is $\lambda$, which is the finite rate of increase, which in other words means that this is average per-capita multiplication factor per one time-step.
When we measure population growth in time-steps of 1 lifetime, we can conclude that $\lambda=R_0$. We actually look at $\lambda$ as at $\frac{N_{t+1}}{N_{t}}$, where $N_{t+1}=N_{t}+B-D$(1) and $N_t$ is the amount of individuals in the populations at time-step $t$. This way we define $\lambda$ using $b=\frac{B}{N_{t}}$ and $d=\frac{D}{N_{t}}$: $\lambda=\frac{N_{t+1}}{N_{t}}=\frac{N_{t}}{N_{t}}+\frac{B}{N_{t}}-\frac{D}{N_{t}}=1+b-d$.

All fine when we deal with ideal conditions, where all mother cells divide and there are no mortalities or mutations.

But suppose we're told that only 80% of the mother cells will divide, and the remaining 20% will die without division. In this case: $R_{0}=0.20*0+0.80*2$.

What I'm trying to understand, how will $\lambda$ be affected by this? Does $\lambda$ refers to ideal conditions only, or it depends on the natural situation?

(1) We ignore Immigration and the Emigration at this point.

*It's been several years since I've worked with similar equations. The following reply is based on memory, and if anyone has a firmer grasp of the materials, please modify or answer as you see fit.

I would assume λ is under ideal conditions or as an average of whatever species you're working with. Your modified lifetime reproductive output still leaves out many variables which can affect λ. By your own words it leaves out mutations and daughter cells that are dead-on-arrival. There could also be predation or conditions where the Mother-cell produces more than one Daughter-cell, resulting in R = 3 instead of 2 and your subsequent λ also being 3. UCLA Bioengineers have actually observed up to 5 daughter cells in cancer lines.

I'm not sure what you mean by "... or it depends on the natural situation?", but ultimately reality is always more complicated than basic equations usually describe. Either B or D can increase or decrease, depending on the species, environment, and how you define t.

Your equation still produces a population increase, just at a slower rate than your ideal conditions. If you're asking if there's a specific definition for "λ" referenced in your equation, I'm not aware of any specific definition for "λ" - it's not a Constant.

Your title question - does the rate of increase depend on mortality - is ultimately "Yes." If mortality is higher than the birth rate, then you will see a decrease of the population until extinction is reached if there isn't an equilibrium or rebound.

However, most populations change at an Exponential rate - NOT Geometric. To that end, you might be interested in the r/K Selection Theory and how they operate within Exponential equations (which are similar to your Geometric equations). In short, r-Selection is the reproductive strategy of producing extraordinary amounts of offspring with a very, very low survival rate. However, because so many are produced you only need a small overall percentage of survival to maintain or increase populations. The tapeworm I mentioned above is one of the stereotypical examples. K-Selection represents species that invest additional resources into raising a few offspring, usually just a handful that are carefully watched over and raised by the parent(s) until they are capable of reproducing themselves. Humans, elephants, most birds, and larger animals in general are K-selected.

For r-Selection your B and D will both be very high, and for K-Selection both B and D will be low. However, both will result in a positive λ simply because it's all about the ratios.


What is the purpose of getting a rabies vaccine after exposure? After exposure to the virus, it is already inside you and your immune system will start to recognize it. Is the vaccine then just a way to kickstart this process so the body can fight off the infection sooner? Is it just a way to introduce much more antigen to the system than would be present only a few hours post exposure from actual virus replication? Or is the boost coming from adjuvants?

Rabies virus enters the body, typically from a bite, and then enters nerves which it follows up to the brain. An immune response to a first exposure of a pathogen generally takes many days, perhaps weeks, to develop to the point where it's protective. This is often even slower when the pathogen is in nerves, which are relatively sheltered from the immune system, and when there's only a small amount of virus present.

After rabies exposure, people are given two treatments: They're given  rabies immune globulin, which contains pre-formed antibodies against rabies, and they're also given the vaccine.

The rabies immune globulin is the most important of these. It provides immediate protection, beginning within minutes of injection. If the virus has not yet entered the nerve cell (which often takes quite a while) then this globulin will bind to and inactivate all, or almost all, of the virus.

Giving the vaccine as well is an added precaution. It will give a faster, probably much faster, response than would the natural virus. There may be only a few rabies viruses present -- it only takes one! -- and of course the natural virus is doing everything in its power to avoid making a strong immune response, whereas the vaccine is the opposite. It has large amounts of antigen, and it's optimized for making a strong immune response. (Rabies vaccine post-exposure is boosted on days 3, 7, and 14 after the first dose. That's an extremely aggressive vaccination procedure that you don't see with any routine treatments.) The vaccine might drive a protective immune response within a few days, while the natural virus might take a month, or never.

If the rabies immune globulin doesn't catch all the virus, or if it temporarily blocks it but then some escapes -- then the vaccine-induced immune response might protect them.

CDC page on post-exposure vaccination
CDC page on post-exposure globulin


If a "parasite" is growing on a dead part of the host or on a completely dead host, does it still count as a parasite? What I mean is the case where the parasite does not contribute to the death of the host (tissue). Instead, the parasite may start growing after the host (tissue) is already dead.
I came up with this question when I was following the link in this answer and read the PDF about a fungus on a fungus on a fungus on a tree. In the PDF, the author first says that the Hypomyces was growing on the dead bracket mushroom, and then says again that Rhinotrichella globulifera was in turn growing on dead portions of the Hypomyces.
I'm not a mushroom expert and the author also does not mention whether the parasites caused the death of their respective hosts.
So suppose the parasites only started growing after the death of the host, do they really still count as parasites? My understanding is that a parasite should seek a host that is not dead and try to leech nutrients without killing the host too quickly (at least until the parasite is ready for the next stage of its lifecycle and no longer needs the host).

In parasitic interactions, one species (the parasite) benefits from the interaction while the other (the host) is harmed. So, whether an interaction is parasitic or not really depends on whether on the host species is harmed by the interaction. If something only grows on the dead remains of another organism, but causes no harm to living organisms in terms of growth and reproduction, it would not be a parasite, and might actually be beneficial to that organisms in some ways.
However, dead cells or tissues are not always useless to a still living organism. For example, the vast majority of cells in a mature tree are dead, but are still important for the survival of that tree by providing structure and water/nutrient transport. A hypothetical parasite could feed only on the dead cells inside of a tree and still cause harm to that tree by weakening it's trunk or impairing it's ability to transport water and other nutrients.
Not knowing much about fungal physiology myself, I can't say whether these "hyperparasites" are truly parasitic or not. But it is at least feasible for a parasite to only grow on the dead portions of a host and still cause it harm.


General transcription factors vs. DNA Binding transcription factors I know that DNA binding transcription factors are trans-acting, but what about general transcription factors?
Are they cis or trans acting?

When we say trans we mean that a diffusible factor, or agent is involved. So a molecule synthesized at one location, that can have a regulatory role in another location in the cell is said to be a "trans-acting" factor.

When we say cis we mean physically linked to, in such a way that the biological regulation only affects other molecules that are attached (in other words, something that is "cis-acting" cannot be freely diffusible).

So prokaryotic operators or promoters, and eukaryotic enhancers and promoters would be examples of cis-acting sequences, or elements.  All protein transcription factors, or even DNA-binding proteins, are therefore trans-acting.


Regarding detection of pregnancy during post mortem Is it possible to detect pregnancy in a woman who is dead considering the fact that she did not a have a showing belly.

Answer is obviously yes. Here's an article reporting a forensic method used to detect pregnancy using placental markers in a Reverse Transcriptase PCR from a DNA sample. It could be applied in a death body, when it's possible to get a DNA sample from a tissue.


Why is methylcellulose used in pharmaceuticals? Why is methyl cellulose used as a pharmaceutical excipient? Is it due to certain chemical properties? What are the reasons for relying on the chemical properties of methyl cellulose?

Methyl cellulose is a dry binder. It is used to make a pill with a small mass of active ingredient and as much binder as required to make the pill a manageable size.

The following properties make methyl cellulose a good dry binder:

inexpensive
non-allergic
vegetarian
soluble in cold water
non-digestable
nontoxic

Most of this information is from the Wikipedia article.


Question about cutting gene in Plasmid I am designing a researching proposal for the class. Because it uses microinjection to up-regulate the gene in C. elegans, the plasmid pCFJ104 - Pmyo-3::mCherry::unc-54 sequences has been chosen. But because the plasmid already has a unc-54, I wonder if there a way that to cut the unc-54 out of the plasmid?

Following the link you provided confirms that the C. elegans expression vector will express your insert of choice in the transgenic animals' pharyngeal muscle cells (driven by the myo-3 promoter).

From examining the two images of the plasmid's restriction map on the page you linked to, I infer that a SacI x XbaI double digest should excise the mCherry insert, and be suitable for sub-cloning your fragment of choice.

However you will need to confirm this for yourself. In general, I think it extremely unlikely that you would find an individual on Biology SE who could provide such precise information as "what enzyme sites should I use for my sub cloning experiment."

A general approach would be to

Research to find out if you can obtain a fasta file containing the complete DNA sequence of the starting plasmid.
Search GenBank to see if there is a record containing annotations for the starting plasmid sequence--that will tell you the start points and end points of each functional region.
If the plasmid is not in a sequence database try using the sequence in a BLAST search of a Non-redundant sequence database. In this example you would have retrieved high scoring hits on the unc-54 gene, the myo-3 gene, the mCherry gene, the beta-lactamase gene from pMB9/pBR322/pUC, and the E. coli lacZ gene (among others).
You should also consult the original publication (if there is one) because it may contain additional useful information, including how to contact the authors--who may have sequence files, useful maps, etc.
With the sequence in hand you will be able to create your own restriction map using a suitable software program (there are many commercial ones), e.g. the EMBOSS suite of open source bioinformatics software.

In your case most of this work was done for you because the AddGene site had two annotated restriction maps that showed almost all of the information you needed.  N.B. One map had the locations of the useful restriction enzyme sites, and the other map had the annotations showing the extent and locations of the worm fragments and the reporter gene. It was only by integrating the information from both maps that I was able to suggest one possible solution to your query.


Why doesn't T5 exonuclease have endonuclease activity in Gibson assembly? Gibson assembly uses T5 exonuclease to chew back the 5' end of dsDNA to generate overhangs. However, T5 exonuclease, in contrast to lambda exonuclease, is reported to have ssDNA endonuclease activity (https://www.neb.com/products/m0363-t5-exonuclease#tabselect0). Why doesn't his cause problems during gibson assembly? Is it just because these don't yield viable assemblies? Or is it because this activity is inhibited somehow, such as the T5 concentration is too low?

The buffer conditions used in the reaction also mitigate against the endonuclease reaction, so it should not be a problem if you stick to the protocols exactly. I've worked on this enzyme since 1988 and was the original "cloner' of the overproducer see http://www.sayers.staff.shef.ac.uk/fen/   for more information on these enzymes
Jon Sayers, University of Sheffield.


Should I design a primer to detect virus based on NCBI genebank? When I searched HIV on NCBI gene bank, I found 2 results from 1997: http://www.ncbi.nlm.nih.gov/genome/?term=HIV. HIV can change every day, so I think the sequence from 1997 is not useful. Is it?

Any other database better than NCBI ?

A lot of people overlook some sub-databases inside NCBI and search the main nucleotide database only.

If You never tried it, you can blast the HIV sequence which You have found, against other databases. On the ncbi blast webpage, just choose the options other than nucleotide collection (nr/nt). I tend to find new sequences in Expressed sequence tags (EST), Genomic survey sequences (GSS) or Whole genome shotgun contigs (WGS). Some of these databases cover unfinished sequencing project and should be a source of new data.

(I am a plant person, not virus person, so maybe you will find out, that different databases are worth searching for you. Or you will find it a waste of time.)

BTW, now some time had passed since your question. How did you solve Your HIV sequence problem ?


How does the nucleophilic attack in DNA replication occur? Hi there,

I am confused about how the nucleophilic attack occurs in DNA replication.I watched this video from a biology professor (https://www.youtube.com/watch?v=y4hKibS2fAo)

I watched this video which stated that during DNA replication, the hydroxl group forms a covalent bond with the phosphate and the two phosphorus groups are a leaving group.

I understand the basics of these kinds of reactions, but this one just seems confusing. I can see that the oxygen which was part of the hydroxl group forms a covalent bond with phosphorus. But what happens to the hydrogen? And why does the the double bond and position of the HO change position from the first picture to the second picture?

There are also some pictures which show water being produced. But the video states that the hydroxl group is forming a bond with the phosphate group. How does that work?

Thanks a lot

Polymerases uses a two-metal ion mechanism to carry out the addition of a new NTP to a growing RNA strand. Two Mg2+ ions are used in this process; metal ion A is involved in the formation of the nucleophile (O-) for the SN2 reaction to occur and metal ion B is involved in the stabilization of the transition state in the reaction. For the addition of a NTP to a RNA strand to occur, an activated 3’ hydroxyl group (O-) acts a nucleophile and attacks the alpha phosphate of the incoming NTP. The reaction is initiated by a deprotonation event. Metal ion A aids with this deprotonation as it reduces the pKa of the hydroxyl (so it is more acidic), making it easier to deprotonate and form the nucleophile, the proton is accepted by a nearby aspartate residue (not water) - doi: 10.1021/ja403842j. After the hydroxyl attack, the mechanism proceeds through a pentacovalent transition state like in a standard Sn2 reaction and the pyrophosphate group (PPi) is kicked out. The image is not mine but comes from this paper: https://doi.org/10.1038/34542, which is quite good, as is this paper: doi: 10.1074/jbc.274.25.17395 and this one https://doi.org/10.1016/j.molcel.2006.03.013


How is the beginning of an episodic memory encoded in the brain? before asking how information is stored, I need to understand

how does episode start and end are determined by the brain ?
how do i remember a movie ?

can you suggest a link to article addressing this issue

thanks

We don't have a full understanding of how episodic recall really happens in the brain, but there are theoretical approaches to understanding memory that are supported (but not shown definitively - it is really difficult to design appropriate experiments that are not beyond current technological capabilities) by experimental evidence. These approaches don't require any sort of hard "start" or "end" signal for episodic memory to work. In these approaches, an episodic memory is thought of as a sequence of brain states that correspond to previously experienced states.

The sequence occurs because connectivity promotes the network to progress from State A to State B to State C, etc. Additionally, all of the states consisting of that one "connected" memory are also associated, so that they prime one another.

To recall, you don't need to start at State A - you can start anywhere in the chain, and just recalling State C will prime you to also recall State A and B, so you can mentally "rewind" the memory a bit (we have no idea how exactly this type of conscious control works), even though it progresses most clearly in the A->B->C sequence.

The point of entry that allows you to initially get in to this chain might not be part of that episodic memory, either. For example, maybe you see a cat, and this leads to to an episodic memory of one event you shared with your own cat 5 years ago.

Brains are very dynamic, they do not behave like a feed-forward computation you might implement in a simple computer program. It is possible that there are "start" or "end" signals for episodic memories that we haven't found yet, but they may not be necessary at all.

For some further reading you could look for references on attractor networks, pattern separation and pattern completion, and theories of memory formation.

The book by Dayan and Abbott on theoretical neuroscience is also a good approach to some of the more basic background and includes an introduction to biologically-inspired models of learning and memory.


Why is the chordate nerve cord described as hollow when it appears to be solid? My textbook says arthropods have a double, ventral, solid nerve cord. And chordates have a single, dorsal, hollow nerve cord.
What is hollow exactly in a cord that looks like this?

Your book is talking about an embryonic structure, the neural tube. This structure forms from an invagination of the neural plate, a collection of cells on the dorsal surface of the early embryo. The process forms a hollow neural tube that will eventually develop not only into the spinal cord but also into the entire CNS.

(image from https://commons.wikimedia.org/wiki/File:Neural_Crest.png)
There is still a lot of development to happen at this point: the cells making up the neural tube will divide many times and proliferate to create the central nervous system. Within the section that becomes the spinal cord, hollow part remains and becomes the central canal, contiguous with the fourth ventricle in the brain and containing cerebro-spinal fluid:

(image from https://commons.wikimedia.org/wiki/File:1313_Spinal_Cord_Cross_Section.jpg)
(note: I had a bit of trouble finding an image showing stages of spinal cord development with a license suitable for posting here, but you can find a bunch if you image search for "spinal cord development". Some examples: https://www.medicalimages.com/stock-photo-illustration-of-spinal-cord-development-within-the-embryo-atweeks-five-a-eight-b-and-ten-c-image22427030.html https://www.brainkart.com/article/Development-of-the-Spinal-Cord_18920/ )


To measure frequencies of eosinophils and neutrophils in airways I am reading this paragraph about RS killed-vaccine in Encyclopedia of Virology, Third Edition (2008), vol. 3, pp. 70-77

What is this data called by which you can say that the frequencies of eosinophils and neutrophils increased within airways?

I think sample is first taken from throat and cultivated on some general culture (blood agar).
Then, specimen is looked under microscope.
Similarly done for the sample after vaccine.
Then, visual comparison with identifying visually eosinophils and neutrophils.

Is the conclusion made based on culturing, microscopy and visual sampling by eye?

Mass spectrometry

I am not sure anymore if this technique is useful at all.
Mass spectrometry can give different intensities and masses.
If so, the intensity of the corresponding peaks should be greater after the vaccine.
Can this kind of conclusion be made based on mass spectrometry?

Interesting would be to know the exact spectrum of eosinophils and neutrophils after the vaccine. I think they do not increase proportionally.
The one increases more than the other.

The original tests where done with blood and then:

  An eosinophillc index was calculated by multiplying the percentage of
  eosinophiles found in the routine white blood count by the total white
  blood count. An index of greater than 250 was considered positive.

See table 8 in this paper: "Field evaluation of a respiratory syncytial virus vaccine and a trivalent parainfluenza virus vaccine in a pediatric population." So they measure the eosinophils in the periphery not in the airways.

This article used histologic techniques: "Respiratory syncytial virus disease in infants despite prior administration of antigenic inactivated vaccine." Both articles are from 1969.

Newer studies used micropical techniques and FACS analysis, but these experiments were done with mice: "Respiratory synctial virus infection in BALB/c mice previously immunized with formalin-inactivated virus induces enhanced pulmonary inflammatory response with a predominant Th2-like cytokine pattern."


Are identical twins clones? Identical twins have the same genetic make up but they differ in development so are they in a way clones?

Are identical twins clones?

A clone is an individual that is genetically identical to another (see wikipedia > cloning). As you said, identical twins (better called monozygotic twins) are genetically identical to one another and therefore an identical twin is a clone indeed.

The role of the environment

Be careful, to not think of clone (incl. monozygotic twin) as individuals that look exactly alike or behave exactly alike. Even for traits that are highly heritable, environmental variation is causing a lot of phenotypic variation and two monozygotic twins do not encounter the exact same environment and can eventually grow up to be very different people. Note that the two blastulas will differ a little bit in concentration of proteins, fats, developmental factors and other things. Such small differences can have important impact on the development of the fetus.

See this post on heritability to have a better understanding of the underlying environmental variation explaining phenotypic variation in populations.

But they are clone for life, right?

Well, it depends on the exact definition of clone but it is important to understand that the expression of genes varies a lot in response to the environment. See for example wikipedia > epigenetics. Also genes may change slightly as we age (see Can genes change as we age?).


What is the literal meaning of the scientific name for the cactus wren? What does the scientific name Campylorhynchus brunneicapillum mean? I simply want to find a way to decipher the meaning of scientific names. In the past I had to translate the names syllable by syllable using an abbreviated Latin dictionary to get a rough idea of the meaning. I can not find an on-line Latin translator that works - and not all scientific names are Latin.

According to the Helm Dictionary of Scientific Bird Names:

Kampylos, καμπúλος (Greek): curved, bent;
Rhynchos, ῥύγχος (Greek): bill.

Also, for the specific epithet:

Brunneus (late Latin): brown;
Capillus (Latin): hair.

Page with the Genus name: https://books.google.com.au/books?id=-RfSBAAAQBAJ&lpg=PP1&pg=PA87#v=onepage&q&f=false

Page with the specific epithet: https://books.google.com.au/books?id=-RfSBAAAQBAJ&lpg=PP1&pg=PA78#v=onepage&q&f=false


How many nutrients do trees process daily? Is this tree fact below that I have found on social media sites true? I don't know the source of the quote. It's pretty amazing. I'll be glad if someone can provide the source too!

Natural Wonders
Every day, a 40 foot tree takes in 50 gallons of dissolved nutrients from the soil, raises this mixture to its topmost leaves, converts it into 10 pounds of carbohydrates and releases about 60 cubic feet of pure oxygen into the air.

I don't know much about trees, but I was very skeptical about this post at first. If this web page is correct, then the post is actually not so far-fetched.

Trees are amazing. According to the page, the average tree absorbs 10,000 gallons of water and uses 1000 gallons, evaporating the rest. 24 gallons of water contains one pound of dry matter. That means that the average tree would accumulate almost 42 pounds of dry matter in a single day.

Now, I certainly cannot vouch for the credibility of the website, but it was difficult to find a page that showed the numbers, so take it with a grain of salt and try to find other sources that back it up or counter it.

Here's the link: https://www.thoughtco.com/process-of-using-water-by-trees-1343505


Is there any format for official Physiological/Medicine answers? Assume you have an exam which has 5 extensive questions and 60 minutes.
You do not have time to cover most if you write everything in essay format.
If you start to write essays, you do not really have time to cover all mechanisms and so on.

I just heard that one student did the exam with by list format, for instance

  sitting -> venous return down & skeletal muscles not working correctly -> trombus.

and then describing relevant mechanisms similarly and combining the their roles shortly.

Another morphology of H. pylori

  Curved (spiral shape), Gram-negative, 2-4 micrometer long, coccoid forms in older cultures,

Is there any official standard or unofficial accepted way how to answer questions in Physiology/Medicine?

Given the highly variable nature of such processes and systems, it's unlikely that a common standard is feasible or sensible. In medical questions, a bottom-up order like in your example usually makes sense, starting with the most specific known cause and deriving from there until you arrive at the symptoms. Treatments can branch off or into the order at the point where they apply logically.

If your exam instructions ask for flow text, your question is alreay unnecessary - but if you believe you have the choice, use a note format that is appropriate by common sense. You are essentially creating a diagram, and like any diagram you have to ensure that it is self-contained and comprehensive.

You can shorten the amount of time it takes to write sentences by reducing the literary quality. Of course a well-written text is more pleasing to read and mark, but the main emphasis in your grading will usually be content, meaning that you can afford to form sentences of repetitive structures or lacking logical connection if it is difficult to figure out quickly whether there is one or how to express it etc.


Will new proteins incorporating new amino acids trigger an immune response? This article reported that scientists have succeeded in adding two new bases to the quartet of A, C, G and T, resulting in non-canonical amino acid. Additionally, the bacteria in which this was done were able to produce new proteins using the newly added bases. The article quotes the scientists as saying that the extra amino acids “might become building blocks for new drugs and novel materials”.

My question is that if new proteins are made from amino acids that don’t naturally occur, won’t the body reject them?

Introduction

This question has two components. The first is the near rhetorical question whether proteins with unnatural amino acids will be considered by the immune system as ‘non-self’. Unless, by chance, the unnatural amino acid resembles some normal macromolecular component, the answer is obviously that it will be regarded as ‘non-self’.

The second question is, to my mind, much more interesting, but does not appear to be considered (or has been taken for granted) in the answer by @Astrolamb. This is whether the immune response would cause such artificial proteins to be eliminated, if  administered therapeutically. It is important, at this juncture, to emphasize that proteins containing unnatural amino acids as the result of expanding the genetic code do not, in principle, raise any problems of immune ‘rejection’ that have not already been seen in ‘unnatural’ proteins containing normal amino acids. Any immune response should therefore be regarded as being to ‘non-self protein’ and rather than to ‘non-self amino acid’.

As there have been many such studies with the latter proteins (and with proteins containing unnatural amino acids introduced by chemical modification) there are extensive studies on which to base an answer. An immunologist would be a better person to do this, but in the absence of any “immune response” I will attempt an answer from my perusal of the literature, leaning particularly on:

K. Wals and H. Ovaa “Unnatural amino acid incorporation in E. coli: current and future applications in the design of therapeutic proteins” Front. Chem 2, 1–12 (2014)

and

B. Leader  et al. “Protein therapeutics: a summary and pharmacological classification” Nature Reviews Drug Discovery 7, 21–39 (2008)

I welcome comments suggesting improvements or corrections.

Summary

The question asks:

  “if new proteins are made from amino acids that don’t naturally occur,
  won’t the body reject them?”

which I take to mean:

  “if new proteins are made from amino acids that don’t naturally occur,
  won’t they induce an immune response which will render them
  ineffective?”

The brief answer to this is:

It depends — the immunogenicity of foreign proteins varies.
Even if an immune response is elicited this may not necessarily render such proteins ineffective.
In some cases the therapeutic intention is actually to provoke an immune response — to make a weakly immunogenic protein more so.

Foreign proteins vary in immunogenicity

The crux of the answer to this question lies in the following:

  The fact that a protein used for therapeutic purposes differs from
  those in a human subject does not in itself mean that it will invoke
  an immune response.

Let us consider two examples to illustrate this.

The first is the case of porcine insulin, which has been administered to patients for many years, but has one amino acid different from human insulin. Regarding such non-human insulin this review states that “severe immunological complications occur rarely, and less severe events affect a small minority of patients”.

The second example is taken from more recent work by D-A. Silva et al. in designing artificial proteins. (See also Nature News & Views summary). They designed mimics of the cytokines, interleukin-2 and interleukin-5, that had extensive differences in helix organization and amino acid sequence from the native proteins. However they reported that “Immunogenicity against the de novo designed proteins appears to be low”.

It turns out that  a wide variety of factors affect the immunogenicity of foreign macromolecules, so that even if a therapeutic protein elicits an immune response it may be weak enough to allow the therapeutic action to occur. In the work just cited, Silva et al. suggest that the reason for the low immunogenicity might be “the small size and high stability” of the proteins on the basis of previous work they had performed with 20,000 mini-proteins.

Admittedly, in some cases a strong immune response will occur and can obviously be a problem, so that measures need to be taken to reduce the immunogenicity. This is widely recognized and discussed in the following paper:

V. Brinks et al. “Immunogenicity of Therapeutic Proteins: The Use of Animal Models” Pharm Res (2011) 28:2379–2385

Sometimes chemical modification of proteins can actually reduce their immunogenicity, as is the case for polyethylene glycol in relation to interferon (B. Leader et al. review, cited above).

Use of therapeutic proteins to provoke an immune response

One use envisaged for modified proteins is in cancer immunotherapy. In brief, the objective is to try to make the body mount an immune response against cancer cells, which may exhibit ‘foreign’ tumour antigens. However, in many cases these differences from normal cells are not sufficient to provoke an adequate immune response. It is has been shown that modifying retinol binding protein by introducing an unnatural amino acid can help overcome the self-tolerance to tumours in mice, suggesting a possible use in cancer immunotherapy  (J. Grünewald et al. “Mechanistic studies of the immunochemical termination of self-tolerance with unnatural amino acids” PNAS (2009) 106, 4337–4342).

Conclusion

Proteins containing unnatural amino acids as the result of expanding the genetic code do not, in principle, raise any problems of immune ‘rejection’ that have not already been seen in ‘unnatural’ proteins containing normal amino acids or chemically modified amino acids. The problem of potential immunogenicity is widely recognized and has been extensively studied by those wishing to develop the considerable therapeutic potential of all such proteins.


Are nucleic acids found in cell membranes? I've found various results online and I was recently marked in on an important test as wrong when I made the assumption they were not found in the cell membrane. Does anyone know what the correct answer is in this case?  Thanks in advance.

Nucleic acids are not structural components of cell membranes (ribosomes and nucleus are the main places where they are found).

However, being open system, cell exchanges chemicals with its surrounding and cellular membrane can transport nucleic acids as well. This is why these acids can potentially be detected in the cell membranes.

If you have the exact question expression it can help with more precise answer.


Since RNA viruses and retroviruses all have high mutation rates, why do only a few viruses have the virtue of variability? We have been taught that it's difficult to make vaccines to influenza, HIV and HCV because they lack the proofreading mechanism, hence have high mutation rates. But most RNA viruses and retroviruses are still antigenically stable, such as measles, rabies, polio, yellow fever, HBV etc. So why do only a few viruses successfully become variable? Is it because their receptors allow flexibility, or their glycoproteins have sophisticated conformations that allow more mutations?

The high mutation rate is only a small part of the reason it's hard to make vaccines against those RNA viruses.  The real problem is not that they mutate rapidly, but that they can tolerate high levels of variation in their antigenic regions without losing fitness.  Viruses like polio and measles, as you say, have mutation rates easily on a par with influenza or HIV, but when they mutate antigenically significant regions, those new viruses are much less capable of infecting and transmitting between hosts.  Vaccines therefore either block the virus replication altogether, or force them into a much weaker form that is much less infectious.

Why do some viruses tolerate antigenic changes better than others? It's not known, but presumably there has been selection for it in those lineages.


Is there a map of the individual motor axons in the limbs? As of right now, I can only find a map of nerve fibers, but not necessarily the individual neuron axons.

For example, here's a map of the nerves in the arm and hand.
http://www.innerbody.com/anatomy/nervous/arm-hand

No it is not possible to map axons at that fine of a scale between individuals.

You mention a possible use for controlling bionic arms. There are a bunch of problems with that approach.

Like @kmm says, at the fine level there is a ton of variation.
I think you are failing to appreciate just how many axons there are, even going to a particular muscle; while each muscle fiber only gets input from one axon, there are thousands of fibers in a single muscle.
The EEG-based approaches to prosthetic control are most relevant when there is a problem with spinal function, for example caused by an injury. In this case, there is no connection between the motor neurons and the brain.
Axons often degrade if their targets are damaged. Therefore, if a hand is lost in an accident, for example, the neurons projecting to the muscles of the hand will atrophy.
If the axons themselves are in place, there are already prosthetics that operate based on muscle contractions in existing muscles. It takes some time to train users to use these devices, but most movements you make involve all sorts of muscles you may not realize are involved, and it is quite possible for brain plasticity to allow muscles in, for example, the shoulder, to control a bionic hand after an amputation.

If for some reason the issues I raised don't apply, there is another alternative: mapping. You don't need to know which axons you want information from, you only need to be able to record their activity (which you will need anyways to operate the prosthetic). Record the activity while the patient tries to move their finger, for example: now you know the signal you should transduce into a finger movement. The technical challenge, then, is being able to isolate that signal from all the other signals from all the other axons in the same nerve. This challenge is related to, though not precisely the same as, the challenge of isolating a signal in the EEG.


Are there any traces for evolution in modern humans over the last 100 years? I ask that because I had a biology class and my teacher said something about a bone in the back of the head that apparently every male has, and for some reason, in the last 20-25 years, its started to fade away and so even though my father has the bone I don't. Or when I was still in high school, and I had to do X-rays for braces the doctor told me that I don't even have wisdom teeth? Are those traces of evolution or are they just random mutations?

Spotting evolution over only 4 generations would be very difficult. You certainly wouldn't see an entire bone disappear in that timeframe, though it might be slightly smaller in average people today than it was several generations ago. Over the timescale you're describing, the only real option is epigenetic changes, which might not be permanent enough to "count" as evolution.


Name of human language related gene I'd like to know the name of a gene with the following description of effects:

Humans having two copies of this gene with a certain mutation aren't able to acquire human language, but otherwise their intelligence is not depressed
The human version of the gene differs significantly from the one found in the great apes
The human version of the gene was transferred to mice, and it was reported that the "voice" and the communication of the so-manipulated mice differs from the one of "wild" mice
If I remember correctly, the gene has the letter "x" in it like hox or pox or pax but alas, memory can be faulty

What is the name of this gene?

Bonus question: What are relevant publications concerning the gene described?


Does homology of a trait necessarily imply that the most recent common ancestor had the trait? If two different species have a trait that is homologous, does this mean that the most recent common ancestor necessarily had the same trait?

Yes, assuming you treat the term strictly.

The term homologous implies that the most recent common ancestor had the trait, although it would be possible for the term to be used in error, when something thought to be a homology is actually not.

If the trait is shared but the trait evolved separately twice, instead you would refer to it as an analogous trait rather than homologous; analogous traits are often the result of convergent evolution.

I can imagine some edge cases, however, where one could argue about homology, although I don't have a specific example in mind (maybe someone can help me out if they can think of one). Imagine you have a trait that is present in an ancestral population, becomes minimized in a common ancestor, and then multiple species descending from that ancestor start to exhibit the trait again. This is called atavism. In some ways, atavism could be seen as convergent evolution and an analogous trait: each has separately evolved that trait from the last common ancestor. However, one would expect a lot more genetic similarity than other examples of convergent evolution and therefore outside of cladistics it might be more appropriate to think of it as a homologous trait in that you can find some ancestor that shared the trait, it just doesn't happen to be the most recent one.


Why are most mutations recessive? Why are most of deleterious mutations recessive in nature? I understood that if it's recessive then one reason may be that the mutant gene doesn't code for a functional protein and so there is no  phenotype to express.  But why is it recessive in the first place?

It is a bit ironic that you phrase your question with 'in the first place'. There is a parsimonious explanation for the effect: Dominant deleterious variants are quickly removed by purifying selection whereas recessive deleterious variants can "hide" in individuals that carry a dominant neutral/advantageous variant.

You can think about it this way: In heterozygous carriers (in which the other variant has a neutral or positive fitness effect), a recessive deleterious variant has no (strong, depending on the dominance coefficient) negative effect on fitness and therefore, in those heterozygotes, purifying selection will not remove the variant (efficiently, again depending on the degree of dominance) - it can only act on homozygous carriers of the recessive variant. A consequence of that is that the recessive deleterious allele usually segregates at low frequency with most carriers being heterozygous.

In short: This probably has little to do with there being more recessive deleterious variants per se (even though that might also be the case due to the mechanisms you described in your question). In the snapshot we are looking at when we investigate genetic data, the likelihood of finding dominant deleterious alleles is way lower than finding recessive deleterious alleles as the latter usually just persist for a way longer period of time.


Are diplobacillus physically connected? I know that a diplobacillus is a bacillus bacteria that has a buddy 'attached' to it.
What I haven't been able to determine is exactly how is it 'attached'? Are their cell membranes fused - are they even touching? If they aren't fused, what keeps them together? Also, does this make diplobacillus a multi cellular organism because there are multiple cells in this organism?

I couldn't find anything about diplobacilli, but I did find some information on Streptococcus pneumoniae, which has been extensively studied. S pneumoniae (R6 strain) normally occurs as diplococci. Electron micrographs—see here and here—show that the two cocci of a pair share a portion of cell wall. This is a result of incomplete separation during cell division. Also, mutations in peptidoglycan-hydrolysing enzymes have been shown to produce longer chains of cocci.
Presumably, something similar holds for diplobacilli.
Calling these bacteria 'multicellular' might be inappropriate, because multicellularity implies at least some division of labour: the cells perform different functions in a cooperative manner. Diplobacilli (such as Moraxella lacunata) or diplococci have not been shown to have such a division of labour, as far as I know.


(Bioinformatics) Protein-Protein Software Prediction I'm trying to figure out Protein-Protein interaction of two proteins without known crystallography structures. Any way software can predict this without the known structure? The problem is most software that does it is just textmining through articles, I was seeing if they can do some sort of prediction based off of just known sequences and other trivial things?

This review about protein docking will hopefully get you started.

Xue, L. C., Dobbs, D., Bonvin, A. M., & Honavar, V. (2015). Computational prediction of protein interfaces: A review of data driven methods. FEBS letters, 589(23), 3516-3526.

There is a page where they provide a short description about the different algorithms used, as well as links to the web servers. I also believe that most of these website should have a downloadable source code that you could compile and use on your own computer/cloud.

Here is a brief summary of the main methods highlighted by the paper:

Homology-based methods. In this approach, biological properties of a query protein are inferred from its homologs. The assumption here is that homologs share significant similarity in their sequence, structure and functional sites. Therefore, this approach performs best when close homologs are available.

Template-free machine learning methods. In this approach, machine learning algorithms are used to classify a target residue as either interfacial or non-interfacial, based on properties of both the target residue and the neighbouring residues. This approach is best used if there is limited availability of homologs, or when templates are not available or of poor quality.

Conclusion: If you have the sequence data available, then the 2nd approach seems most appropriate. You could also apply both methods and see the extent of agreement/disagreement between the methods, i.e, you could use the machine learning approach to detect the interfaces, and subsequently validate your docking predictions based on sequence data, if close-enough homologs are available.


How many species did Carl Linnaeus classify? How many species did Carl Linnaeus (senior) classify?

More than 13,000.

Plants: >9,000 names.
In Systema Naturae 10th edition, commonly taken as the starting point of modern taxonomy, Linnaeus is reported to have published around 6,000 plant names (I haven't counted, but Müller-Wille gives 5,900 and Stearn says "almost 6,000". The Wikipedia figure of 7,700 may come from a different edition of Systema Naturae).

However, that's just SN10. Luckily, a wonderful source has compiled the names from all of Linnaeus's work:
The Linnaean Plant Name Typification Project of the Natural History Museum says that Linnaeus published more than 9,000 valid plant names in his life (names that are still valid under current nomenclatural conventions), and they have many of them in a searchable database with references to where Linnaeus published them.

Animals: >4,200 names.
For SN10, different authors give 4,236 or 4,378 animal names. Stearn says "nearly 4,400", so perhaps he too was unsure. The total number Linnaues described in his life is probably higher, as he did write separate zoological publications like Fauna Svevica, but I couldn't find a source like the project bringing together all of his animal names.

 Müller-Wille S. 2006. Linnaeus' herbarium cabinet: a piece of furniture and its function. Endeavour 30: 60–64.
Stearn WT. 1959. The Background of Linnaeus's Contributions to the Nomenclature and Methods of Systematic Biology.)


Correlation of non-coding DNA with coding DNA I sequenced the first exon of the MC1R gene of 15 labradors (genomic DNA) to look for the loss-of-function mutation (C.916C>T) and as expected, it was where it should have been (916th base pair). As i compared the SNPs with the phenotype of the dogs i found a second mutation that also correlated 100% with the phenotype of the dogs. The mutation is located 45 base pairs before the start codon of the first exon. As far as i'm concerned the region that lies right before the first exon should not be part of the coding DNA. If so, why could this mutation have been evolutionary conserved? Or am i simply mistaken in that the mutation before the first exon could also be part of the gene for MC1R (meaning there would be an intron before the first exon which i'm not sure if that's possible)?

If you have 2 different mutations (irrespectively of where they sit in regards to the final gene-product), and both correlate perfectly with a given phenotype, (and you have dismissed any other potential cause), you can not formally say, if the first mutation, or the second, or both mutations are required for your phenotype. (Though you can make educated guesses or rely on external information...)

Loss-of-function mutations do not have to be in the protein-coding region (but simply in one part of the genome, which is required for the expression of a gene towards a phenotype).

Polymorphisms can also be neutral - especially in artificially bred / selected animals, such as the wolf-like animals we now call labradors. You could easily envision a scenario where some neutral mutations was present in an individual, which would have a desirable / selectable mutation. If that neutral mutation is within a few 100bp of the selected mutation, it unlikely will have been uncoupled from the selected trait / mutation.


E value cutoff for RNASeq search I am trying to narrow down the possible search criteria from an RNASeq experiment. I already have the cds sequences so I took these and used Blast+ program to blast the data against itself to find sequences that were the same.

From what I have read the E Value is based on the database size. My database only has ~27,000 sequences in it, does this mean that only exceptionally low E values will be relevant to me? Are there any other criteria I should search for before writing the program to eliminate similar sequences?

Going by an e-value or bitscore cutoff will give you possible homologs, but it sound like you want to remove redundant sequences. If you want to cluster and combine similar sequences to make a smaller database, you could just go via sequence identity using something like CD-HIT. This, for example, is what's done to produce the UniRef set from the UniProt database.


If cells regularly renew, why do we have scars? Question may sound bit poetic but I have a pretty basic question here: Often we get a minor wound and cells renew and quickly "cover" it. But when we have deeper wounds, often they leave behind scars. Why does it happen?

I was researching around and saw this comment on a related question:

  That's not true - some cells turn over quite quickly, others take months or years, others never replicate.

But how come we get some wounds "completely filled", while others leave scars on almost the same skin/body part? And ok, if a deeper cut has resulted in inner (different type of cells) being damaged, why do we find the scar on epidermis?

Thanks a lot for your guidance.

Scar tissue formation is part of the normal healing process in which fibrous material braces and pulls the wound together, in other organisms (and young mammals) this process is mild and just serves to temporarily reinforce the damaged tissue as new cells migrate in to begin replacing the missing tissue, sometimes to the point of replacing missing limbs in lizards and amphibians. However in adult mammals and birds the process of fibrous tissue is far more exaggerated, creating longer lasting or even permanent scars, Here the wound keeps filling in with more and more fibrous tissue instead of moving on to regenerating what was there originally. This dense fibrous tissue often prevents new cells from easily migrate into the tissue, essentially stalling the healing process. It seals the wound much faster than the more mild deposition of other animals but can often prevents replacement of the fibrous tissue which would otherwise happen as the missing tissues is regenerated. This mass of fibrous tissue is what we call a Hypertrophic scar. this is why scars can also fade, as cells often can migrate in and slowly replace the the matrix but this is severely limited by the dense packing.

Note there is a second rarer form of scar tissue that can form, called keloid scarring. This form of scar spreads beyond the original wound area and seems to be caused by some form of runaway extracellular matrix deposition. It should also be noted adult mammals sometimes do regenerate decent portions of tissue, albeit not well, possibly because some of the controlling cellular signalling machinery has be lost or reappropriated. All the factors that affect this are not understood and are a main focus researched. We do know it varies quite a bit from tissue to tissue and is not terribly consistent.

It is believed that mammals and birds develop this stronger matrix deposition which leads to permanent scar tissue becasue healing fast is more important for them than healing completely since their metabolism runs so much higher. They can't wait around for it to heal they need to get moving as soon as possible or risk starvation,additionally a stable body temp makes for a more inviting environment for bacteria so sealing the wound is paramount. Thus sealing and mechanically reinforcing the wound is more important than regeneration. As you can imagine the worse the injury the more important it is to plug it fast which is why minor injuries are less likely to scar. This is also why lizards and amphibians end up with less permanent scars they can take the time to better regenerate the tissue. Of course this is difficult hypothesis to test, however there has been some success in getting mammalian tissue to regenerate more by removing scar tissue as it forms or just preventing collagen production.

Evolution is one lang story of "good enough" and scar tissue is good enough functionally that the speed at which it can seal a wound favors it over slower regeneration.


Mechanism of Decorticate & Decerebrate Posturing? Also why is only Decorticate Rigidity a misnomer? I read these two from various books, and got confused. The confusion is -

Reticulospinal tracts control gamma motor neurons. Gamma motor neurons control tone of muscle.
In decerebrate rigidity, the reticulospinal tracts are cut, so the gamma motor neurons start firing excessively, and SPASTICITY develops. I understood this part and why Decerebrate Rigidity is a misnomer as it is actually spasticity.

Question is, in decorticate rigidity, the cerebral cortex is damaged. The basal ganglia are intact. One explanation I found is that the basal ganglia keep the reticulospinal tract activated so gamma motor neuron is under control. But if basal ganglia have no direct communication with brainstem or spinal cord, and their efferents pass through cerebral cortex, then even in decorticate rigidity, the reticulospinal tract should not be working, and thus the gamma motor neurons should fire excessively, in which case the decorticate rigidity also becomes a spasticity.

Am I missing anything? I am keeping red nucleus and vesticular nuclei out of this just to make matter simple. My question is about activity of gamma motor neurons in these two conditions. I hope you got the question. Thank you.

1)

a. Decorticate posturing means rubrospinal tract is the dominant output to the motor neurons of the body... maybe dominant is the wrong word, I am not all that knowledgable on this subject, but it is certainly altering the standard reticulospinal tract based extensor posturing.

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

It is responsible for the strange flexion of upper limbs (aka arms). I say strange because when you think coma you think extension, not flexion. The lower limbs (aka legs), as always is extensor. Why the upper limb but not the lower limb? The red nucleus may play an additional role in controlling muscles of the shoulder and upper arm via projections of its magnocellular part.

b. In decerebrate posturing the rubrospinal tract is also cut, since the lesion is below the red nucleus. In this scenario the reticular activating system (aka reticulospinal tract) is the dominant output to the motor neurons of the body. Here you get the classic extensor pose, for both upper and lower limbs...

The point is: Rubrospinal tract was what you were missing. The red nucleus is the specific part of the basal ganglia that is involved...

2)
the difference between spasticity vs rigidity:

spasticity is an increased resistance to the passive movement of a
joint due to abnormally high muscle tone (hypertonus) which varies
with the amplitude and speed of displacement of a joint.
rigidity is an increased resistance to the passive movement of a joint which is
constant throughout the range of joint displacement and not related
to the speed of joint movement.

your supposed to test this out on patients to get a feel for what's the difference.

spaciticity is the case for upper motor neurons lesions (ex. stroke), since the spinal reflexes are not being inhibited from above...

an example of rigidity in neurology is Parkinson's disease, which is the loss of the substantial nigra, which like the red nucleus is also in the midbrain... while the the substantial nigra and basal ganglia loop do influence the motor control of the body... they are not upper motor neurons. Upper motor neuron is specific to the corticospianl tract, it is the neuron going from cortex to anterior horn of spinal cord. Basal ganglia does influence the motor cortex but it isn't part of the corticospinal tract, hence not an upper motor neuron lesion.

3)
Role of muscle spindles in spasticity from upper motor neuron lesions:

I am using this website for this part of my answer:

http://www.d.umn.edu
it's from university of minnisota, which is funny because their acronym is UMN

  high resistance to stretch occurs when the spindles are overactive
  (usually due to high rate of gamma motor neuron discharge) -->
  HYPERTONIC (SPASTIC)

  removing inhibitory inputs to the gamma motor
  neurons increases their discharge rate, and increases spindle output

  this can happen when there is an UPPER MOTOR NEURON lesion

It seems that with an upper motor neuron lesion, the gamma motor neuron is uninhibited, thus the gamma fibers have a constitutively increased discharge rate and muscle spindles are overactive. The machanoreceptors in the spindles then decrease their afferent sign, which should lead to relaxation of a/g-motor neurons, and well, I dunno, I am thoroughly confused on the precise mechanism of UMN lesion causing spasticity. Reflexes are intact so the a/g-motor neurons should relax, since only UMN damaged and not any part of the reflex arc. I seem to be missing something here.

I'm calling for back up, someone please help!


How do DNA, enzymes, hormones etc. reach their proper cellular locations? I was trying to understand DNA transcription from this chapter, and there seems to be no explanation on how exactly the proteins, enzymes and other molecules manage to find each other inside the cell. How do they get attracted to each other in order to start reactions or transcriptions?

Same way, when the body secretes a Follicle Stimulating Hormone, how does it reach the follicle instead of losing its way in the bloodstream and ending up in a woman's feet or getting excreted out of the body? In minute 20 of this video, the person speaks of how medicines are first "sent" to the liver, but this MIT article says that medicines go all over the body.

At least for a wound it's an understandable process. An artery of vein is severed and any blood that was supposed to flow through it now can't, so there's an accumulation of white blood cells and antibodies there which can disable any intruders (though I'm sure they wouldn't be able to see an intruder and move toward it, but rather just probabilistically bump onto the intruder), and if the intruder enters the bloodstream it would probabilistically bump into other WBC's or antibodies and get killed. Else there's always fever to kill them.

Similarly, one study says sperm use heat sensors to find the egg. Another assumes it's a chemical signal.

I went through the information about cell signalling, signal transduction and allosteric regulation, but although they speak about receptors, they don't explain how the chemicals manage to find those receptors. It's like saying that I entered a huge college campus and found the secret place where my friends were meeting and they receive me when I met them, but there's no explanation on how I knew which way to travel in that huge campus to reach my friends. Given how accurately DNA transcription happens and how viruses know to shed their shell on entering a cell and make use of the cell's transcription mechanism, I believe there has to be a specific process through which these molecules "know" how to find these receptors. Is there any research that could throw light on it?

The answer given by Sadegh gives a general correct broad view. But one part of the puzzle is missing, which is molecular recognition.

Molecules bind to each other via physical/chemical interaction like forming hydrogen bonds, electrostatic interactions and other mechanisms. The sum of all interaction defines the strength of the binding. If molecules have enough interactions, they stick together otherwise not.
Mind that all these interactions have a range of action (a field). Like with magnets, two opposite magnetic poles attract each other at a distance, before they get in contact. Imagine a small molecule getting close to a receptor, if they are "magnetically" compatible they will be attracted toward each other.

Indeed, molecules in the bloodstream (like the Follicle Stimulating Hormone) flow all around the body. However, not all the molecules end up in all the cells. That is because cells have specific receptors on the surface that bind selectively their target. In the case of the Follicle Stimulating Hormone, some cells, like the Sertoli cells or the granulosa cells have the right receptor able to bind that specific hormone.

In the case of a drug targeting the liver, the drug gets assimilated or injected into the bloodstream, it travels all around the body but it is retained by specific molecular interactions only (mostly) in the liver. It is not that the drug knows where the liver is, it is just forced to pass through it and then it is retained by it. The drug passes also through the lungs, but it has no affinity for them so it doesn't get retained.

Inside the cells, it occurs the same. Molecules pass all around, but they do not stick to anything unless a specific protein/receptor/enzyme is found.

There is an intricate network of interactions both inside and outside the cells, molecules randomly flow throughout this network bouncing on each other until they find the binding partner and they stick to it.

Randomness is not the only factor. Brownian motion occurs, but molecules are also actively moved by different chemo/physical stimuli causing the network of interactions to be in fact extensively regulated.

For example, during the cell cycle, the cytoskeleton is actively remodeled to favor the flow of certain molecules in determinate directions (look metaphase). The cell can also alter its own permeability, actively influencing the influx/efflux of a variety of molecules.

At the body level, the circulatory system itself forces the flow in a specific direction (from the stomach to the liver for example).

The fact is, that there are mechanisms to selectively control the flow of the molecules at any level in the body, from organs to tissues, to single cells and inside subcompartments of the cells. The topic is complex but very well understood.

I suggest a big dive into this book if you really want to get a grasp on how biological systems work.

UPDATE: As suggested by @WYSIWYG, the picture would be more complete adding a very short note (the topic is way to broad to be extensively discussed here) on chemokines which are a perfect example on how cells can respond to concentration gradients. Chemokines act as a chemoattractant to guide the migration of cells. Cells can sense the concentrations of chemokines in the surrounding environment and, usually, move toward the source of the signal following the increasing concentrations of the signal molecule. In general, it cannot be overstated the importance of chemical gradients during embryogenesis, inflammation and countless other events. Gradients effectively indicate to cells the path to follow.


Can Western Blots be used to quantify the activity of a protein? I am new to Western Blot analysis and I have recently done my first two. I am studying a phosphoprotein (a protein kinase) that can be both activated and inactivated via phosphorylation at a specific amino acid residue. I have labelled my membrane against the active and inactive forms of my protein of interest (using phosphospecific antibodies), as well as the total protein (using pan-specific antibodies).
I know that Western Blots are used to quantify the expression of a protein (i.e. how much of a specific protein there is in a sample). But I was wondering how they can be used to quantify the activity (e.g. how functional the protein is) of a protein, e.g. how can I measure/determine whether my protein is more active/inactive in my treatment samples vs. control?
For example, I have normalised the integrated density values for my active protein bands against the integrated density values for my total protein bands. Then I have calculated the fold change in protein level for my active protein in treatment samples relative to control.
If I have observed that the fold change for my active protein is reduced by 40% (as an example) in treatment samples relative to controls, would this be sufficient data to say that the activity of my protein of interest is reduced in treatment samples compared to control?

I see 3 parts to a complete answer:

If you define the phosphorylated protein as active, and non-phosphorylated protein as inactive, and you have a total protein blot (as you say, via pan-specific antibodies) as you describe, then you have done everything correctly.

It's simple math from there on based on radioactivity or fluorescence or mass or whatever you use to quantify your band intensity. The 3 components should match up with the inactive protein amount (active + inactive = total). If this is consistent, you have additional evidence that you have done it correctly.

However, here come the hidden assumptions: this is all assuming that (i) you are not experiencing significant protein loss during your preparation steps, that (ii) your antibodies are good (specific and yield the complete protein extract), that (iii) the blotting procedure is performed correctly, and most importantly, that (iv) your initial definition is valid, that the phosphorylated protein is truly the active form of the protein, and that the unphosphorylated counterpart is the inactive form. You see, this is not always the case, though with some (most?) kinases, it is. If it has not previously been demonstrated, one may raise the reasonable objection that your assumption is wrong. However, I take it that in your specific case, the kinase activation by phosphorylation is well understood.


Do DNA footprints vanish in generations? Consider humans (or really any creature with sufficiently complex set of genes).  If person $A_0$ has an offspring, say $A_1$, we can without a doubt find markers in $A_1$ that we can definitely say indicate that $A_1$ is the progeny of $A_0$.  Likewise, for any generation $n$ we can say that $A_{n+1}$ has markers that indicate that generation $A_n$ is their parent.  Presumably (and maybe this is where I'm heavily mistaken), as $n$ grows large there are fewer "direct signs" that $A_n$ has $A_0$ in their ancestry.  I mention "direct signs" (although this isn't an official term) because obviously if one can prove $A_{n-1}$ is the parent generation to $A_n$ and $A_{n-2}$ proceeds $A_{n-1}$ and so on ... then one can deduce the relation between $A_0$ and $A_n$.  That's not my point.  My question is this:  Do the genes of $A_0$ "dilute" so that after so many generations it is possible or probable that none of the genes from $A_0$ are present in $A_n$ for some large $n$ (where by "none" I mean "no genes that give us a high warrant for believing $A_n$ is related to $A_0$ in the absence of evidence about $A_j$ for $2\le j \le n-1$").  Obviously if $A_0$ is human and $A_n$ is human then they share a great deal of their genes with one another (something like $99.99\%$)

If there is such an $n$, how large does $n$ need to be so that say $90\%$ of what makes $A_0$ unique is no longer present in $A_n$ (with a high probability of confidence), what about $95\%$ no longer being present, or $99\%?$

Please let me know if my question isn't sufficiently clear (I'm trying to convey the heart of my question, even if it isn't perfectly worded).

You seem to be figuring that since $A_1$ has half the genes of $A_0$, and $A_2$ has half the genes of $A_1$, etc throughout the generations, we quickly get to a point where $A_n$ has none of the genes $A_0$ had.

This would be correct, if we assumed no inbreeding among the descendants. And by "inbreeding" I don't mean siblings or first-degree cousins breeding, but any of $A_0$'s $n^{th}$ descendants breeding with another. Which is clearly absurd; at some point you're going to run out of breeding partners who aren't also a descendant of $A_0$, unless the lineage isn't very prolific and the number of descendants $A_0$ has is always a small proportion of the total population. And in that case, sure, those genes are probably going extinct.

The same thing happens the other way around by the way; we (most of us) have two grandparents, four great-grandparents, etc. As we go back in time this exponential growth quickly outstrips the amount of humans that were alive at the time our $n^{th}$ great-grandparents were around. That's because that exponential growth assumes no inbreeding, which there is. There is a point in time in the past beyond which everybody alive today is the descendant of everybody back then who has any descendant at all; that's called the Identical Ancestors Point. See for example:

https://www.nature.com/news/2004/040929/full/news040927-10.html

The end result is that there are really two outcomes for $A_0$'s descendance: either they increase over the long term faster that the overall population grows, or they increase at the same rate or slower. In the first case, we'll reach a point where the whole population is part of $A_0$'s descendance. In the second, unless population growth is huge then $A_0$'s line is probably going extinct. Even if not, and if we assume individuals are breeding randomly throughout the population (not a good assumption, but no gene dilution without it), then the original assumption that $A_0$'s descendants have fewer and fewer of $A_0$'s genes every generation is correct, and $A_0$'s genes will likely go extinct even if their descendants don't.

On the other hand if $A_0$'s descendance end up consisting of the whole population, then no more "dilution" can occur. Say at that point every individual has 1% of $A_0$'s alleles; their offspring will also have 1% of $A_0$'s alleles on average, and same goes for all later generations.

Note that at that point $A_0$'s alleles are distributed throughout the population; even if everyone has 1% of them, they don't all have the same 1%. So the question of whether "what makes $A_0$ unique" is present in the descendants is really hard to interpret. Some of $A_0$'s alleles may be present in everybody at that point (they have become fixed in the population), some may be present in X% of the population, some may have gone extinct. The specific combination of alleles that made $A_0$ is gone, but then it was gone when $A_0$ died. As for the question of whether scientists can investigate the descendants and find traces of $A_0$ after all those generations, the answer is "sure": see the aforelinkedto nature article.

More to the point, consider this sentence you wrote:

  Obviously if $A_0$ is human and $A_n$ is human then they share a great deal of their genes with one another (something like $99.99\%$)

Do you not see how this factoid relates to your question? You are asking whether human $A_n$ still shares some genes with its ancestor human $A_0$, and caveat that "obviously" they already share most of their genes, what with being human. You mean, what with both descending from the common ancestor to all humans. That those $99.99\%$ of identical genes come from. Except of course that not even, given $99.99\%$ of that $99.99\%$ comes from our common ancestors with chimpanzees, and so on. Most of "what made the common ancestor to all life unique" is still in our genes today! So yeah, it will take more than a human-scale $n$ generations for all traces of a human ancestor to be predictably erased from its human descendants (keyword "predictably"; in practice many lineages and alleles do go extinct, but not all do and you can't really tell which in advance). More than that, on those evolutionary timescales natural selection is a strong force and you get phenomena like conserved genes - that is, genes that are important to the organism and are thus selected for to stay the same. At that point there is no "random dilution" phenomenon happening: there are specific forces at work to maintain the gene in all descendants in a more-or-less unchanged state.


Restriction endonucleases are found in? Quoting from : Scientific American July 1975 The Manipulation of genes by Stanley Cohen :

  Restriction endonucleases (and modification methylases) are widespread
  in microorganisms; genes for making them were found on viral
  chromosomes and extrachromosomal plasmid DNA as well as on many
  bacterial chromosomes.

Why would the genes for making RE be found on viral chromosomes ? Also, could you give some examples where they are found on plasmids ?

If you have a dsDNA genome and replicate it by rolling circle like most bacteriophages and many plasmids do, an endonuclease is pretty much a necessity.


Why do antacids have a special importance when taking lactulose? “Before taking lactulose, tell your doctor and pharmacist what prescription and nonprescription medications you are taking, especially antacids, antibiotics including neomycin (Mycifradin), and other laxatives.” (Quote from here)

Why do antacids have a special importance when taking lactulose?

Other laxatives can exacerbate the effects of lactulose, leading to diarrhea, and could eventually lead to dehydration and general GI issues.

Neomycin and antacids in general raise the pH of the gut, making it more basic, and reducing the peristaltic movements. Lactulose, meanwhile, is broken down to primarily lactic acid (if I recall) in the gut, and creates a more acidic environment. The acidic environment increases peristaltic movement in the bowel, and in turn the patient eliminates waste.

If you are on concomitant antacids or other drugs that raise the pH of the lower gut, you are reducing the effects of lactulose, and in a worse case scenario, making the constipation worse.


How does a sheep's fleece impact its tolerance for high temperatures? I am interested in whether a sheep endures more stress when its environment is hot if it has a full fleece or if it is recently shorn.  Put another way, at the extremes, is a sheep more likely to die due to high temperatures if it has its fleece or if it does not?  If the answer depends on breed, what are the biological differences that cause one breed to interact with this element of its environment than others?
I am interested in temperatures around 90°F but if the answer differs at some temperature commonly experienced somewhere on Earth, that would be interesting to know as well.
I am interested in modest relative humidity values, in the 40%-60% range, but again if the answer differs outside of that range it would be interesting to know about.
I considered asking this question on a physics stack exchange (where a sheep might be modeled as, say, a radiator with or without insulation) but I'm particularly interested in the answer for real, actual sheep - biological processes and all - and not just a spherical sheep of radius r.

Wool serves as a good insulator, meaning it doesn't allow warmth to escape the wearer easily allowing the wearer to remain warm. Furthermore, wool helps maintain a dry environment by absorbing moisture from the air (and sweat) which can also keep you cool during summer.
Here's a link that talks more about this for both wool wearers and sheep: https://shepherdsdream.com/blog/wonders-of-wool/how-wool-keeps-us-cool/


What are the difficulties/challenges against developing a coronavirus vaccine? Multiple groups of scientists are trying to develop a coronavirus vaccine but they are not yet being fruitful. What challenges or difficulties are there in the process that slowing down and/or causing failure in development of vaccine?

There are multiple challenges presented, and many of those are not limited to coronavirus vaccine.

As mentioned above, it just takes time. Before a vaccine can be used in patients, clinical trials must be performed to validate the safety and efficiency of the vaccine candidate. A Clinical trial includes three phases, which again, just takes time.

But to really answer your question, what are some challenges of developing a vaccine?

To begin with, from the perspective of lab research, we first need to develop a vaccine candidate. What protein on the virus should we take as an antigen? There are many many proteins on the virus, and for CoV, we know it is a protein called Spike protein. It is the neutralizing target on the virus. Which means, when an antibody bound to this site, it could prevent the virus from infecting the cells. Okay, then we have to know, do we need to do something to this protein to make a vaccine? For example, when we try to manufacture this protein into a vaccine, what if the protein is degraded? Or it somehow becomes a 'bad' protein that simply cannot stimulate immune responses in human? These are just some examples of roadblocks of developing vaccine.

Let's suppose we finally work those out. Then what's next? Each candidate vaccine needs to be tested in animals before going into human clinical trial. This step is time-consuming.

Now we are finally ready to start clinical trials. According to FDA, the vaccine for human trials (also for each drug) needs to be produced under Good Manufacturing Practices (GMP). It's basically a standard operating procedure to make sure that the vaccine candidate can be manufactured in a large-scale, quality-controlled manner. There are many many challenges, like how to purify the protein? How to scale-up production. This is partly of the reason why the first vaccine in trial in USA is an mRNA, and in China is a DNA, both of which does not require complicated protein purification.

As you can see, the list of challenges can go on and on. But there are scientists and doctors working diligently on it. Hopefully we'll get there.


Why does strenous exercise cause vision of "lights"? I had a hard climb a week ago. I got so tired then any time I closed my eyes I saw these lights inside my head. I see these lights almost every time that I run fast or some thing like that. What are they and where do they come from?

Here is a picture I drew using Photoshop ;)

This is a common phenomena which most of us come across. Seeing flashes of light, stars and other shapes in the eyes occur when the body goes through stressful activities. For example while you are climbing the blood flow will be more to other prominent parts like hands and lower waist so brain and eyes will get less supply of blood as well as nutrients. Hence those flashes or stars are visible to us. This phenomena is called "Phosphene" and a phosphene is a phenomenon characterized by the experience of seeing light without light actually entering the eye.
Wikipedia/Phosphene gives an explanation for occurrence of Phosphenes:

Phosphene is "seeing stars", from a sneeze, laughter, a heavy and deep cough, blowing of the nose, a blow on the head or low blood pressure (such as on standing up too quickly or prior to fainting). It is possible these involve some mechanical stimulation of the retina, but they may also involve mechanical and metabolic (such as from low oxygenation or lack of glucose) stimulation of neurons of the visual cortex or of other parts of the visual system.

So seeing flashes of light can be due to:

Blood shifting.
Low blood sugar(causes weakness).
Head trauma.
Headache.

So to summarize this thing, we should have enough nutrients, water supply to the body whenever we come across stressful activities. Phosphenes are temporary stuff which do not harm eyes.


What preceded ATP synthase? ATP Synthase is ubiquitous throughout life on earth and so most probably evolved within the last universal common ancestor (LUCA) before that lineage diversified into the various kingdoms of life.

It is suggested that the functional domains comprising the ATP Synthase complex were cobbled together from pre-existing sub-units, each with with a related activity (e.g. the union of a proton motor with a DNA Helicase with ATPase activity), which seems reasonable, although a bit vague in the details.

The fact that a primitive ATP Synthase arose in the first place suggests that ATP already had a central role in cellular metabolism and so begs the question, what preceded ATP Synthase in the role of generating ATP in the LUCA cell?

There are metabolic processes in which ATP is synthesised without the involvement of ATP synthase. The best examples are, in fact, two steps in the glycolytic pathway, catalysed by phosphoglycerate kinase and pyruvate kinase. This is why, in the absence of any aerobic metabolism, many organisms (like yeast for example) can grow quite happily, producing two molecules of ATP for each molecule of glucose that is metabolised.

Presumably this process is what enabled ATP to gain its central role in energy metabolism without any need for an ATP synthase.


In endochondral bone formation, why does only hyaline cartilage get ossified to form bone? There are three types of cartilage: hyaline, fibrous and elastic cartilage.
Fibrous cartilage does not have perichondrium...so it does not take part in ossification because perichondrium needs to develop into periosteum.
Hyaline cartilage has more matrix in comparison to elastic cartilage. Hence, during ossification the quicker spreading of calcification of the matrix will lead to the death of the chondrocytes which will develop into osteoprogenitor cells. Is my theory correct?

yes this is correct, i think hyline cartilage gets transformed to bone more quickly due to the fact that is has the matrix which is closest to bone in terms of density, also the cells are located more closely, therefore it is easier to convert this tissue to bone.


Outbreeding depression in humans Is there any evidence of outbreeding depression in human beings?

Answer below is copy-pasted from the section Do we have documented cases of outbreeding depression? of my answer here.

Many cases of inbreeding depression have been documented in humans (McQuillan et al. 2012, Strauss et al. 2013, Lettic et al. 2008, Gellera et al. 1990) but cases of outbreeding depression seem much rarer if any!

I spent some time screening through the literature searching for potential evidence of outbreeding depression. The only paper I found is Udry et al. 2003.

Udry et al. 2003:

First, note that they do not place their results in the context of our present discussion and do not talk about outbreeding depression.
They report that children of "mixed-race" in US colleges report having more behavioural troubles. One would obviously note that there could well be true that "mixed-race" children experience a different environment (incl. social environment) than "non-mixed-race" children. Such results therefore does not suggest the existence of any outbreeding depression.
They also reports more skin problem in mixed-race children. Unfortunately, 1) their p.value is only slightly significant and 2) they track tens of variables without correcting for multiple comparisons and only one came out significant suggesting it is likely to be a false positive.

So, in short: No, there is little to no evidence of outbreeding depression in humans

It is not impossible that there is a publication bias in which researchers looked for inbreeding depression more than for outbreeding depression but I doubt it would be the case. Such bias seems possible only if the outbreeding depression, should it exist, would be very slight and hard to detect outside a rigorous scientific study. In essence, such potential publication are impossible to detect.


Which processes are included in the process called cells eating themselves? I am reading about atrophy and I am thinking to which processes the phrase cells eating themselves refer to.

  Cells need something to survive these difficult times. To decrease
  protein synthesis to survive. If insufficient, cells start
  to eat themselves. Then, ubiquitine-proteosome pathway and autophagy
  pathway.

I am not sure if it is only apoptosis.
It can refer here to longer cascade.
I think it can at least refer to autophagy where one cell degrades its components.

Which processes does the phrase cells eating themselves include?

So:

the processes are mentioned in the quote you provided: "ubiquitine-proteasome pathway (note: it's proteAsome) and autophagy pathway". As far as I know, apoptosis per se is not utilized for recycling.


A tool to get annotation features by position in the reference genome Previously, when I needed to find a genomic feature (promoter, CDS, repeat etc) that underwent mutation (SNP) I used my own scripts to load an annotation file, parse it, map the SNP's position and output the sequence of the feature. Now that I'm moving from microbes to mammals with huge annotations, introns/exons and huge genomes, my scripts don't work that well and I'm sort of lazy to optimize the code or rewrite it in a faster language, since I'm sure there should be some prominent tools for the task. That's it, could you recommend me some tools that do the following:

Given a reference genome, annotation and a VCF (or similar variant file) match the SNPs to genomic features in the annotation
Output the entire feature that underwent mutation, e.g. if the SNP happened in a protein-coding gene, I need to have the entire protein-coding sequence not just an exon/intron.

Thanks in advance.

Well, after 2 weeks and several thousand lines of code I got a demo-version of my revamped annotator up and running, but then I was told to take a look at SnpEff. The tool makes everything I was to implement in my own one, so if anyone ever wants to annotate SNPs with regard to genomic features they hit and possible effects, give SnpEff a try. It's really fast.


Is it known how human sweat glands evolved? If human descends from apes than probably we lost our hair. Perhaps in the age of homo erectus we lost our hairs and began transpiring through our skin with sweat glands. But how did these glands evolve? Is it from another kind of cell which is similar?

I am not sure exactly what you are after when asking "how did these glands came?". It seems that you wrongly believe that similar glands do not exist in other primates. Here is a short answer that will help you to search for more information about the evolution of these glands.

Chimpanzees and Gorilla also have sweat glands. The use of sweat gland in thermoregulation is however quite unique to humans and is thought to have evolved in parallel of hair loss and bipedism. See The evolution of sweat glands (Fold and Semken 1991) for more information.


What is a 21q21 deletion? I am reading a journal paper about the relationship between the protein NCAM2 and autism, and I have come across the following statement:

We report three patients affected with neurodevelopmental disorders
and harbouring 21q21 deletions involving NCAM2 gene.

I am not sure what a 21q21 deletion is. I have read that 21q refers to long arm of chromosome 21, and that 21q21 refers to position 21 on the long arm of chromosome 21.
However would a 21q21 deletion, refer to this whole section of the chromosome being missing, with this section including the NCAM2 gene? Any insights are appreciated.

I would suggest looking more into karyotype nomenclature; it is admittedly a bit odd. Here is one related question/answer that puts it in context.
I haven't looked at the paper in detail but generally what it means is that there is some cytologically relevant big chunk of chromosome that is missing that roughly overlaps with the chunk of chromosome that we find at band 21 of chromosome 21 (not position 21). Note that these cytobands/karyotype/G bands visible in a chromosome spread under a microscope, so these are quite large deletions.
Looking at the paper methods, it is clear that in 2/3 cases they confirmed the deletions by looking at karyotype data (FISH/chromosome spreads):

For Case 2, CNV confirmation and parental studies were performed by metaphasic and interphasic FISH on leucocytes using BAC RP11-43A6 (chr21:18,414,905e18,567,253, hg19 build). For Case 3, CNV confirmation was performed by G-banded karyotype. Parental studies were not available.

The terminology is quite outdated now as usually we are looking at sequence data these days, which has much higher resolution, but a lot of the stereotypical chromosomal abnormalities still carry these confusing names. And seeing it on a chromosome under a microscope is still the gold standard for these large chromosomal events.


Using ion-exchange chromatography to purify DNA from a cell extract - Is DNA more negatively charged then RNA? When applying this method we have a glass or plastic column of resin which is positively charged. Then we pour cell extract into the column in order to capture the negatively charged particles which include DNA.

After that we gradually add salt which neutralizes the molecules. But it does this gradually so strongly attached DNA molecules fall last while RNA and proteins fall first.

The question is why does DNA have a greater negative charge than RNA ?

A longer or duplexed Nucleic acid will have more charge per mole of the molecule. But generally it is not the overall charge that matters in electrophoresis or MS or chromatography; it is the charge density and specific charge (z/m) that matters (charge density of a longer RNA will be almost same as smaller RNA. they will also have same specific charge)

The properties of stationary phase  is very important in controlling the separation process. Without knowing what resin is used, it will be difficult to comment about why RNA is not retained.
Sometimes the strong basicity of the stationary phase, such as in quaternary ammonium resins, degrades RNA by alkaline hydrolysis.

If yours is a commercial resin then you will have a tough time finding out what exactly it is made of. Unless of course you break the column open and do a molecular analysis of the resin :P


PDB file SEQRES have different data? In PDB file, SEQRES represent the aminoacids but some pdb file present the "GLC" and some other.
for example

SEQRES   1 A   26  GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC
SEQRES   2 A   26  GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC
SEQRES   1 B   26  GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC
SEQRES   2 B   26  GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC

In that PDB ID: 1C58
What are this and What are represent the SEQRES?

The pdb file that you mention is entitled:

  V-Amylose at atomic resolution: X-ray structure of a cycloamylose with 26 glucose residues (cyclomaltohexaicosaose).

So, it isn't a protein at all, it is a circular oligosaccharide consisting of 26 glucose (GLC) residues. I imagine that the usual fields in the pdb file have been fudged to accommodate this.


Why was it so hard to decode the corn genome? My teachers growing up told me it was impossible to decode the maize genome. But yet its been done.

Why was decoding the genome so significant, and what made it so difficult?

The short answer is that corn genome is large and has a huge amount of duplication events. Around 80% of the genome are repeated. It's hard to assemble genomes with large amount of duplications because our sequencing technology, practically, at best can give ~500 base pairs. Figuring out the ordering of duplicated regions relies on scaffold sequences or comparative assembly to rice genome.