Optimization of E. coli growth in D₂O (heavy water) I would like to find a method of increasing the biomass of my D2O cultures because my current method is not yielding enough protein. I would like to also minimize the amount of H2O in my culture.

My current methodology is a small scale growth of 3mL with 75% D2O and LB grown for approximately 9hrs. This culture is then used to seed a 20mL 100% D2O and M9 culture overnight and this entire culture is used to seed a 1L D2O and M9 culture.

Thanks for your time.

It looks like you're very stringently avoiding $^1\mathrm{H}$. You may want to consider replica plating your transformations onto $\mathrm{D}_2\mathrm{O}$ plates (selecting for $\mathrm{D}_2\mathrm{O}$ tolerance earlier.)

I assume you're doing protein NMR and want "triple labeling." Depending on how specific your carbon labelling is, you may want to grow your starter cultures on triple labeled agal hydrolyzate (something like "Bioexpress.") You can buy some unlabeled stuff for fairly cheap (\$55 USD at CIL for 10 mL of 10X stock) and if your starters grow well you can spring for the same quantity of $^2\mathrm{H}$,$^{13}\mathrm{C}$,$^{15}\mathrm{N}$ for around \$405.


Identify This Plant (Flower) I just bought this plant from flower shop, after it flowered it was very beautiful red flower, can anyone tell me what is this flower?

This is a Gerbera, which belongs to the daisy family (Asteraceae). Compare:

There are various species.

  The domesticated cultivars are mostly a result of a cross between Gerbera jamesonii and another South African species Gerbera viridifolia.[5] The cross is known as Gerbera hybrida. Thousands of cultivars exist.

(from Wikipedia)


How do pineapples and lemongrass grow? You can't plant the leaves, you can't plant the fruit, but, if you plant the part where leaves and fruit meet you will grow a whole pineapple plant.

The part of the pineapple where the leaves meet the stem is the point from which the whole plant seems to form. Cells below seem to become fruit and fruit skin, cells above seem to become leaves. If you look at a cross-section of this part of the plant you can see the way that the cells seem to move outward from this point.

(1)But is that really how it grows? Are the new cells added from the center or do new cells get added to the leaves at the tips and in the middle of the leaves?

(2)I know some orchid roots grow from the tip... but is this the case for all roots?

(3)I noticed that some lemongrass in my worm compost bin has grown roots! So, I transplanted it outside. Maybe I can grow lemongrass. Again, it was the part of the plant where the roots met the leaves that still had life in it.  This seems like a very powerful part of the plant. Is there a name for the part of a plant from which everything else grows?

UPDATE: http://en.wikipedia.org/wiki/Meristem

This is what the regions is called! But I still want to know if the plant "pushes" out the leaves from this central point or not... and are all root like orchid roots that grow from the tips?

First, allow me to provide the link to an old paper that deals with development in Ananas comosus, it should be freely available and answer this question in more detail: http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.1936.tb06884.x/pdf

Now, to briefly explain the observation that a mature plant will grow from the region where the leaves of the pineapple attach to the fruit, it should be noted that the pineapple fruit develops at the top of the central stem of the plant in a developmental process known as influorescence (please see a picture of a pineapple plant). Since the top portion of the fruit is in fact the end of the primary stem, this region contains the apical meristem, a collection of stem cells that are apparently is sufficient to give rise to a mature organism. Pineapple development has apparently been a topic of constant research for nearly a century (due to its economic importance), so there are quite a number of papers that can provide much more detail, but many of these are not freely available.

In nature the primary means of pineapple propagation is the formations of lateral shoots, the growth of which consequently are accelerated by influoresence of the main shoot.

Now the actual way the plant grows is not quite as simple to answer, as plant development is often as complicated as animal development, but in general it is a function of cell division and elongation. In the root apical meristem, there is a region known as the quiescent centre which contains the actual root stem cells. Directly behind the quiescent centre is a region known as the merismatic zone, which features extensive cell division, and directly behind that is the elongation region where the cells grow, effectively pushing the root tip through the soil. In the region behind the elongation region, the maturation zone where the cells have reached full length, cells begin to form more rigid cell walls and differentiate into the different tissues of the root.

The shoot apical meristem is dome-shaped, the top of the dome is known as the central zone and is analogous to the quiescent centre of the root apical meristem, the sides of the dome are the peripheral zone, a region of rapidly dividing cells that give rise to the leaves, and the central region of the dome is the rib zone that gives rise to the stem structures. Elongation, differentiation, and maturation also occur below the meristem region, but involve the additional complexities of leaf organogenesis.

There should be considerable additional information on plant development online.


Allergies - congenital situations or created and developed over the years? This is probably an easy question, but I've yet to find an answer.

Recently I felt under the weather more and more often, especially at the time I was waking up. I assumed this was an allergy-related thing so I did an allergy test and found out that I am allergic to dust-mites. This does explain my condition after waking up, as these mites mostly reside in the mattress and thus affect you during sleep. However, it doesn't explain why this allergy hadn't affected me at all until now and why it suddently appeared after 20+ years. So the question is, is this (and more generally other allergies) a congenital situation, or was it developed due to my way of life, (non) cleaning habits etc.?

Allergies are caused by one's immune system.  If you had never been exposed to the allergen, you would not experience any symptoms.  So they are not innate or inherent.

Why do people develop food allergies after repeated exposure?  I have not read any convincing explanations for the biology behind this.  When you look at the heavy-chain switching that takes place in B-cells, the IgE that are responsible for allergy symptoms are the terminal switch, so those antibody variable regions have already been selected during your life history up until that point.


Is there gas exchange in the fingers? I saw A documentary many years ago that said that hemoglobin will take in O2 in the fingers and toes. I have Not been able to find any information on this. But it would seem that being so close to the surface some gas exchange would occur, and more so in the fingers and toes than the teunk.

At first I was skeptical about this question but then I did some researching and apparently, a certain amount of oxygen is indeed taken up from the surroundings through the upper layers of our skin. In fact, the paper titled "The cutaneous uptake of atmospheric oxygen contributes significantly to the oxygen supply of human dermis and epidermis. states that

  the upper skin layers to a depth of of 0.25-0.40 mm are almost
  exclusively supplied by external oxygen, whereas the oxygen transport
  of the blood has a minor influence.

Here is another paper that you would find interesting. In short, I would say that its not just the fingers but O2 diffusion into cells take place over the whole body.


Why do mushrooms grow in rings (sometimes called "Fairy Rings")? Mushrooms disperse their spore in all direction. Then why is there a formation of fairy rings? Why do they grow in one shape and not randomly?

When spores germinate, they do not generate mushrooms directly, but haploid mycelium starts to grow. Only when the mycelium from spores with the other mating type is met, cells fuse and generate diploid mycelium, from which mushrooms can grow.

Fairy rings are caused by a radial outgrowth pattern of the diploid mycelium, followed by resource depletion in the oldest part (middle).

This page seems to have good additional information about hyphal growth.


How large an expression boost is typical from codon optimization? There are lots of different codon optimization approaches out there, and a lot of different qualitative reasons to want optimization (e.g., organism codon bias, GC content, avoiding secondary structure).
One may also want to avoid optimization, however, in order to increase reusability of a component, comparability with prior results, or opportunities for error.
I'd like to know how much I'm likely giving up if I decide not to codon optimize. For example, in my typical work giving up 10% is likely to be lost in the noise, but giving up 2x is worth thinking carefully about, and giving up 10x means it's a must-have.
I know "it depends", and there's a lot of qualitative information out there, but is there any way to get a good rough-order-of-magnitude estimate of the typical expression boost from codon optimization?

I think that there is a problem with how well current codon optimization algorithms actually "optimize" protein expression. I am not aware of any algorithms that work beyond a heuristic level and so for an arbitrary protein, one cannot predict the expression boost that optimization will provide - sometimes yield is significantly decreased. This review covers some of the complexities of optimization really nicely https://doi.org/10.1016/j.molcel.2020.09.014.


Restriction Mapping - Homework question I have trouble in solving this exercise.

Exercise

  A circular plasmid of 10,000 base pairs (bp) is digested with two restriction enzymes,A and B, to produce a 3000 bp and a 2000 bp bands when visualised on an agarose gel. when digested with one enzyme at a time, only one band is visible at 5000 bp. If the first site for enzyme A(A1) is present at the 100th base, the order in which the remaining sites (A2,B1 and B2) are present is?

Why I struggle with this exercise

How can a 10,000bp plasmid produce 3000bp and 2000bp only on agarose gel. I mean where are the remaining 5000bp? I dont know if my concept is right.

Linearised bands on an agarose gel may be doublet. That can clear the doubts in problem. But still I dont know how to do a reasonable restriction mapping and find out sites of different enzymes.

This is not as hard, as it first seems. Lets have a look at the single enzyme digests first: The digest with enzyme A and B only leads to products which are 5kB (5000 bp) away from each other. Since they are of the same size, both equally sized restriction fragments appear as one band. So each enzyme cuts the plasmid exactly in half.

The double digest is a bit more tricky, but not much. You get two products from it, with 2kb and 3kB. This means that enzyme B cuts between the restriction sites for enzyme A, resulting in these two fragments. Have a look at the sketch I made below (only a quick one and not to scale):

A1 and A2 are the cutting sites for enzyme A, B1 and B2 the sits for enzyme B. The numbers on the outside are the positions on the DNA sequence. You can see that a single digest leads to two fragments of 5kB (doesn't matter which) and that both A and both B sites are located 5kB from each other.

A1 is at position 100, A2 has to be at position 5100, B1 is located 2kB behind A1 (and therefore at position 2100), and B2 2kB behind position A2 (and therefore at position 7100). To get the same restriction pattern it is also possible that B1 and B2 are located 3kB behind their respective enzyme A position (so at 3100 and 8100) and you still get the same pattern of 2kB and 3kB on the gel.


Do phagocytes need antibodies to be able to engulf pathogens (to function)? I recently saw a question about monoclonal antibodies, that are specific to a certain virus, being split (into their constant and variable regions via an enzyme), and the question asked whether some statements were false or true.
One of the statements said that the virus could be engulfed by phagocytes if any were present. The statement turned out to be false and I'm not completely sure why. Is it because phagocytes need fully intact antibodies to function so that they can attach to them via receptors specific to the constant region of the antibodies consequently becoming attached to the virus and so being able to engulf it?
I thought that phagocytes could work on their own and that antibodies just made their job easier. Is that assumption correct?

Phagocytes don't necessarily need antibodies to recognize intruders, i.e. by presence of non-self sugars. Additionally, phagocytes can aid amplification of effective anti-bodies by presenting degraded pathogens to the adaptive immune-system. I found this concise summary of the innate immune system, that I would strongly recommend to read!
Now to your more specific question: Detection of viruses. You have to consider, that viruses are highly optimized to evade the innate immune system:
Viruses can happily replicate and mutate without proof-reading without negative consequences and with relatively low conceptual constraints, as they are so simple, compared to cells. This is why the innate immune-system is prone to miss viruses (at least those, that are optimized for a certain species). Imagine how big of a genome you would need to cover all possible viral substances by at least 1 innate gene! Read about hyper-mutation to understand the role of antibodies to detect even these highly evasive viruses.


Why doesn't surgical steel cause inflammation? It seems some very specific alloys like implant surgical steel and titanium don't cause inflammation in the human body, but when I asked my doctor about it, they simply said "it just has some chemical property that doesn't cause it."

So...what exactly is special about these metals compositions as to not cause inflammation like most other things would?

Some can
First the terms you are looking for is biocompatibility and bioactivity. The study of them is called biomaterial science. Both fields are relatively new so complete answers do not exist, there has been a certain amount of trial and error in find suitable materials.
There are a dozen factors that go into these things, toxicity, whether they corrode in the body, whether they are soluble, chemical reactivity, whether they trigger an immune response, whether they can bond with bone or other tissues, mechanical resilience, steric and electrical properties, wetting, even how smooth it can be made can have an effect. The other important thing is many materials have very different biocompatibility depending how and where they are used, different parts of the body can have very different conditions, for instance material used in a bone screw might be useless in a dental implant (different PH and chemical exposure) or a heart valve (different mechanical and electrical requirements).
Titanium has remarkable biocompatibility with internal bone implant, its already low reactivity actually gets better as its surface oxidizes as it becomes slightly polarized and will incorporate many cellular surface molecules(passivation). Many of the factors that make titanium useful in this way are still being studied.
Surgical steel is a broad term that covers several types of steel used for  multiple medicalpurposes, it includes steel implant and steel only used for instruments. Some forms of surgical steel work great for instruments but are rarely for internal implants, often because the same nickel content that makes them corrosion resistant is also bioreactive, triggering an immune response, but its superior mechanical properties means it still is sometimes used as implants, especially temporary implants were corrosion is less of an issue.  (paper, sorry it is only available in German). Nickel free surgical steels used in cutting implements is stronger and harder (what you want in a medical blade) but  without nickel it will quickly corrode in the body.
Part of the reason your doctor did not know was some aspects are still unknown in general and the study of these properties is rather specialized so a general practitioner may have never studied the parts that are known. Consider an  pilot still know very little detailed metallurgy of their engine components, and still be an excellent pilot becasue they don't really need to know.  Heck most of reason I know anything about it is I used to hang out with a guy who made titanium implant screws for a living and it just sounded kinda interesting so I read up on it.


Is there a difference between sleeping late and waking up late vs sleeping early and waking up early? For example, if I sleep at 1 AM and wake up at 10 AM, will it negatively affect my health opposed to sleeping at 10 PM and waking up at 7 AM?

There is a popular theory that each person has a certain "chronotype" [Ref 1]. Based on your genetics, you could be naturally an early person ("Lark") or a late person ("Owl") [Ref. 2].  What will negatively affect your health is actually fighting what you naturally are.  You probably know which chronotype you are, and if not you can go by what time you naturally sleep/wake when you don't have school/job scheduling such as at the weekend.

[Ref. 1]:Chronotype Review
[Ref. 2]:Social jetlag paper


How is the probability of a sequence occuring with BLAST calculated? What is the probability that a given nucleotide/amino acid sequence will occur in the whole database program BLAST searches in? How this probability is calculated?

According to BLAST documentation statistics of local sequence alignment, when doing database searches, is done

  by treating the database as a single long sequence of length N.

N is therefore a sum of all sequences with varying sizes from a given database.

Underlying assumption is that

  query is a priori more likely to be related to a long than to a short sequence, because long sequences are often composed of multiple distinct domains.

To calculate the probability, we need to choose a scoring scheme (for ungapped example: choose a mismatch penalties), which for a query sequence gives us a statistically significance score $S$. Expected number of alignments with score of at least $S$ follows Gumbel extreme value distribution:

$$
E = Kmn\cdot e^{-\lambda S}
$$

where m is query length, $n=N$ and $K$ and $\lambda$ are distribution params.

Again, according to docs and its references, probability of finding at least one such seq would be $P=1-e^{-E_{(N)}}$, where $E_{(N)}$ is E-number for concatenated N-sequence and query sequence.


Subset of Protein Crystal Structures (from PDB) Is there a well-accepted subset of the Protein Data Bank set of protein structures that:

Has only "high quality" structures (may be differing metrics of this; e.g. resolution, size, or structural completeness)
Has minimal redundancy (e.g. nothing with exact sequence identity from the same species)
Is still as large as possible, spanning as many molecules and species as possible
[Optionally but better] Is not too biased (e.g. certain classes of proteins are highly over-represented in the PDB)

It is possible to download the entire PDB and make up rules for myself, but this seems like something people might have already considered reasonably extensively. I'm hoping for a dataset I can just download and cite, in the best case. :)

Richardsons' Lab has a top8000 list.
See their paper from 2016.

They also have top500 list, but it hasn't been updated for many years.


How do the homologous chromosomes pair up and position themselves along the center of the cell? I am not sure... Most textbooks just state "they line up" but I don't know how... Something to do with the cytoskeleton or microtubules? Thanks for any help

There are many things involved in the pairing of homologue chromosomes.

Before mitosis can occur an important prerequisite must happen: the division of centrosome. This small complex is the principal microtubule-organizing center in the (animal and therefore human) cells. During interphase the microtubules originating from the centrosome, project to the cell perimiter with their + ends (this where they grow). At the beginning of mitosis the duplicated centrosomes separate and migrate to oppsite sites of the nucleus to form the poles of the mitotic spindle. As the nuclear envelope disintegrates the spindle captures the chromosomes at the cetromeres. Since the microtubules are growing from the centrosomes this capture eventually pushes the choromosomes to center. Source: The Molecular Biology of the cell. Fourth Edition. ISBN: 0-8153-3218-1 (hardbound) 0-8153-4072-9 - (pbk).
A searchable online version: http://www.ncbi.nlm.nih.gov/books/NBK21054/

I've found a few good articles with many details:

Current Biology, Volume 12, Issue 17, 3 September 2002, Pages 1473–1483
The Dynamics of Homologous Chromosome Pairing during Male Drosophila Meiosis
Julio Vazquez, Andrew S Belmont, John W Sedat

and
Homologous pairing and chromosome dynamics in meiosis and mitosis
Bruce D. McKee

I took a quick glance at the above mentioned articles, and it seems that homologous chromosomes tend to be close together (paired if you wish) during interphase most of the time.


What kind of bug is in this photo Wondering what kind of bug this is found outside

That is a Ten-lined June Beetle, (Polyphylla decemlineata) in the family Scarabeidae. You can tell its a scarab by its lamellate antennae. The stripes indicate the species.
https://en.wikipedia.org/wiki/Ten-lined_June_beetle


Synthesis of an additional DNA in Pachytene and Zygotene I've read, that in Pachytene and Zygotene additional DNA material is synthesized, about 0,3, 0,1% respectively. Why is it so?

About 0.3% of total DNA complement is synthesized during those 2 stages as a measure of replication repair mechanism.

Reference:

http://www.ncbi.nlm.nih.gov/pubmed/3731943

http://www.nature.com/nature/journal/v219/n5153/abs/219489a0.html


Why do stem cells injected into muscle become muscle cells? In this article published in Science Daily, researchers injected teratoma-derived stem cells into mice with muscular dystrophy, and the stem cells regenerated 80% of the lost muscle. But what is the mechanism that results in their becoming muscle cells, rather than any other type of cell?

I'd have to assume some sort of cell signaling is responsible for this directed differentiation into muscle cells, so what is it? Can it be reproduced in vitro?

Looking at the paper itself, we find that they prepared the stem cells to have myogenic (muscle-specific) properties. They first injected stem cells into the irradiated (which kills muscle stem cells) muscles of immune-deficient mice. This resulted in tumor growth (teratoma - a stem cell derived tumor, where different kinds of tissues are spontaneously formed. Growing in a muscle environment increases the chance of muscle tissue formation.). The tumor cells, which expressed muscle-specific markers, were isolated from the other tissues and then used for regeneration of an injured muscle.

In their teratomas they checked for cells expressing α7-integrin and vascular cell adhesion molecule-1 (VCAM-1), which are markers expressed in satellite cells (muscle stem cells). These factors were expressed in about 10% of the fraction that did not show any hematopoietic and endothelial markers (meaning: there were a lot of other tissues formed as well). They also showed expression of Pax3 and Pax7, which are muscle-specific transcription factors, important for differentiation of myogenic progenitors. These cells were therefore already muscle-specific cells before they have been transplanted for regeneration.

The researchers did, in fact, do in vitro and in vivo differentiation experiments. For in vitro differentiation they subjected their muscle-marker expressing cells to a myogenic medium. This mimics the muscle environment and enables cell differentiation signaling. Here is an example protocol how this can be done. Then they transplanted their muscle stem cells into a muscle and they also managed to differentiate in vivo and regenerate the injured muscle.

The entire process of pluripotent stem cell to muscle cell differentiation can be performed in vitro, but seems to be tricky (1,2). Medium factors or genetic activation of transcription factors can activate different steps in the differentiation cascade.


Why analyse transcriptome instead of proteome? Analysing the transcriptome (RNA-Seq, microarrays, qPCR etc) is probably the most widely used technology to assess gene expression and dynamic cellular processes. The results are then extrapolated (functional analyses, GO etc) to infer biological cellular consequences. RNAs are really only the middle-man. Presence of an mRNA doesn't necessarily mean that it will become a protein. It could be degraded by microRNAs etc. before translation. It is eventually the protein that are actually causal to a biological change.

So, my question is why not just go directly to the proteins. Why not just extract the proteins and sequence them, quantify them, analyse and draw conclusions? What are the compelling arguments to study the transcriptome to understand biological processes?

Q: Why not just extract the proteins…

A: It’s not just a question of extracting the proteins, you would need to separate them and then isolate each of them. There is currently no practical way to do this for say, 10,000 proteins, which in any case may have multiple forms. The beauty of the RNAseq method is that it does not require physical separation or isolation of transcripts.

An approach more likely to be useful is to identify and quantify the proteins in situ, but this is still some way off having the comprehensiveness and sensitivity required.

  Q: …sequence them…

A: Protein sequencing is slow and difficult. It cannot be applied on a mass scale, unlike sequencing of DNA copies of RNA transcripts. Other methods of identification based on physical behaviour (migration or elution position) are more promising, and the direction that is likely to be followed.

  Q: …quantify them…

A: Even that is difficult, when you are eluting proteins from gels, for example. In contast, RNAseq methodology just counts transcripts. (But the likely direction this will go is quantitation by peak height, without separation or isolation, as with metabolomics, or by the intensity of some signal from the protein immobilized in the gel, staining of something more sophisticated.)

So, in general, you do protein analysis on particular individual proteins of interest to you, whereas you can do RNAseq analysis on all the transcripts in a biological sample, and then go fishing (among the results, and afterwards on the lake if that’s your thing).


What does the term 'bioavailability' mean? From what I've read,

  Bioavailability is the degree to which food nutrients are available
  for absorption and utilization in the body.

How would you explain this with an example?

Bioavailability is a concept which applies to nutrients and drugs which pass through first-pass metabolism, i.e. orally (and to some extent nasally) consumed substances. Anything absorbed in the gut first passes through the liver before reaching the rest of the circulation, and both the gut and liver may metabolise it to some extent. The liver in specific has the powerful Cytochrome P450 system, a huge variety of enzymes to break down all sorts of substances, although in some cases it can actually produce more active or even toxic forms instead of breaking them down.

This can lead to drastic reductions in the amount available in the systemic circulation after oral administration. E.g. propanolol (a beta blocker) needs to be given in 100mg doses orally while intravenously (avoiding first-pass metabolism) only 5mg are needed.


Why do I have a lot in common with my mother? I have not spoken to my mother in 15 years but recently connected with her and her side of the family. I was primarily raised in a different sub-culture after the age of 4. As it turns out I "accidentally" have a lot in common with my maternal relatives. We like and dislike many of the same things. Is there some dominate trait in our nature which affects our psychology to cause us to agree on everything from TV, food and lifestyle?

In this answer I mainly repeat the comments!

There are several reasons why you might share some traits with your mother.

genetic (see below)
epigenetic
environmental influence while being in the womb
environmental influence up to the time you were 4 years old
the two environment were not so different (maybe because your adoptive parents wanted to follow the will of your mother or just because by chance your adoptive parents have similar behaviour that your mother)
multiple testing issue (see below)

These reasons can be classified into three categories:

environmental variance
genetic variance
poor observation (statistic mistake)

The phenotypic variance in a population is influenced by the environmental variance + the genetic variance + the variance due to the interactions between the environmental and genetic variances. The heritability can be calculated as the part of the phenotypic variance which are genetically determined. Such calculations make sense only for populations not for a given parent-offpsring pair.

genetic: It does not make sense to ask whether the variance of a trait is dominant or recessive. It makes sense to say that "liking pink" is dominant over "liking blue". Therefore, you should tell us what is the variant of a given trait that you share with your mother. In such case we might tell you if this variant is dominant or not over the other variants. But of course, this works only for traits that are at least slightly genetically determined. liking a color will certainly not have a strong genetic variance for example. And even if a trait is 100% genetically determined, complex genetic architecture might make it hard to answer. For example a given variant might be dominant in a given genetic background but recessive in another. Finally, I should say that it costs to perform the necessary study (Genome Wide Association Studies) to know exactly the part of the variance of a given trait that is genetically determined. And of course, such studies depend on the population we look at.

Multiple testing issue: Without realizing, you actually looked at many different traits. You might have looked at your favorite color, your favorite beer, the way you wash your teeth, the sport you practice, the color of room, whether you are calm or impulsive, etc... You might not have paid attention only to things that match but you would have found as many similarities (not the same ones though) with any other human on earth.


Can the human body utilize electricity? In any way could the body store electricity supplied externally?

No, the human body cannot utilize externally applied electricity.  Applying electricity to the body will either have no effect, if the amount is small, or will disrupt normal functions of the body or cause injury if the amount is larger.

An overview of the effects of electricity (for doctors) can be found in "Conduction of Electrical Current to and Through the Human Body: A Review".


Determining potential protease sites within a recombinant protein My expressed proteins are frequently truncated and I'm trying to figure out which bands are which. The first thing to come to mind is using PeptideCutter from ExPASy but there is just a data deluge of potential sites. I was curious what other strategies exists for determining the potential breaks asides using LC-MS.

LC-MS is certainly quantitative and will give you a definitive answer, but it is costly and requires access to such a machine.

I presume you're analyzing your protein based on western blotting.

The first thing you should always do is verify your DNA sequence is coding for the protein product you want. Once you're sure of this, the western blot will give you an indication as to where your protein is (approximately) being cleaved. Say you protein has a predicted size of 40 kDa and you see a band at 20 kDa, then your cleavage is somewhere in the middle of your sequence. There are a TON of proteases that could be potentially cleaving your peptide and you need to have a hypothesis as to what that could be. Your peptide could be cleaved by an endopeptidase (cutting within), or a carboxypeptidase (C-terminal cleavage) or an aminopeptidase (N-termainal cleavage). To go back to the 20/40 kDa example, it could be your peptide was cleaved N-terminally o C-terminally down to a size of 20 kDa, or that it was literally cleaved in the middle by an endopeptidase.

Something you may consider is the use of a general protease inhibitor cocktail (Roche makes a really good tablet product called Complete and Complete mini tab). These mixes have a bunch of general protease inhibitors which will stop most cleavage events. If you still see cleavage after using an inhibitor cocktail, you can reasonably expect that you are not inhibiting the protease with the tablet (thus narrowing down your search) and then you can better comb through Expasy's PepCutter data. You should also do a literature search to see what has been reported about your peptide or motif.


Do axon grows after cutting/damaging of some of its part? Do axon grows after cutting of some of its part to near original place?

Do axon restores after local damaging of some of its part?

I take https://class.coursera.org/neurobio-001/ classes and learn that axons are very long. So it is interesting if they able to restore connection to far places parts of body...

UPDATE

https://en.wikipedia.org/wiki/Axon_guidance

Well look at this picture from Junqueira histology book:

In an injured or cut peripheral nerve, segments of axons distal to the injury lose their support from the cell bodies and degenerate completely. The proximal segments can
regenerate from their cut ends after a delay. The main changes that take place in an injured nerve fiber are shown in the picture above.
In the nerve segment distal to the injury the axon and myelin, but not the connective tissue, degenerate completely and are removed by macrophages. While these
regressive changes take place, Schwann cells proliferate within the connective tissue sleeve, giving rise to rows of cells that serve as guides for the sprouting axons
formed during the reparative phase.
The axon grows at the rate of 0.5–3 mm/day


Reason for the source of fetal bovine serum What is the reason that perhaps the most commonly used serum in labs is fetal bovine derived? Is there something about fetal serum that is particularly useful over say serum just harvested periodically from adult cows, or cows going to slaughter?

The reason fetal bovine serum (FBS) is used is because it supports a wide variety of cells and really supports their growth.  It has a high concentration of growth factors, but also a low concentration of antibodies.  So it promotes growth in almost any cell or tissue type without also having antibody reactions with it.

Adult cows blood will have the opposite concentrations, higher levels of antibodies and lower levels of growth factors as they have already grown.

There are currently several research projects looking for a alternative or synthetic FBS, but nothing has worked as a total replacement.  There are a few substitutes for specific purposes, but nothing with the diversity of uses that FBS has.


Have there been any positive public health effects due to UV lights? Occasionally, in hospitals and in eating establishments in the US, they have industrial grade UV lights in sconces attached to the wall (though they seem to be less prominent as the years go by).  I understand the anti-microbial properties of UV light, but are these devices anything more than show pieces?

Have there been any lasting, significant public health gains that have been correlated with the use of UV light in public places?

There have been some studies regarding the use of intensive UV light installations in surgical wards or other settings as a anti-microbial tool. Generally speaking, these are part of a general interest in non-cleaning based anti-microbials in hospitals, such as UV light, O3-based machines, and copper/silver coated surfaces.

The answer to your question will depend on what you consider "lasting" and "significant". They're a relatively new technology, and haven't had a huge penetration into the market yet, so the only evidence you're likely to find is hospital-sized non-randomized trials.

So basically, the answer to your question, as I read it, is "No, but..."

There hasn't been an opportunity for these technologies to show any sort of lasting, significant reduction in hospital acquired infections. But there is some promise that these types of technologies, and those like them, may help reduce the burden of infections when they're used appropriately. The current state of research is figuring out just how workable they are, how to best use them, and what they can and cannot be expected to do. That kind of evaluation is actually what I'm doing as part of my dissertation work, though my focus is on the general concept, rather than a specific device.


True or False: Vaccines are designed to protect against invaders that are encountered rarely, not all the time I read the following statement in this article:

  Vaccines are designed to protect against invaders that are encountered
  rarely - not all the time

Is it true? If yes, why?

Not true. Vaccines were initially made for the highly contagious diseases that used to cause epidemics (which obviously means they were not rare).

The efficacy of a vaccine depends on multiple factors which includes adaptability of the pathogen.

The all-the-time encountered pathogen that the article is talking about is HIV; the reason for why no effective vaccine exists for it is because it has high mutation rate.


Why is clownfish attracted to actinia? I heard that Actinia Equina normally eats what it can catch, but this clownfish here doesn't care much about that:

https://www.youtube.com/watch?v=Ughm4mnZ1ls

Since the actinia obviously can't hold the clownfish, clownfish does whatever it wants with actinia swimming all over it. Is the clownfish having some sort of fish fun, or is there a purpose behind this playing with actinia?

It's an example of SYMBIOSIS

Clownfishes(Amphiprion ocellaris) are never found without an anemone as they have this obligate association with them. Although they can survive without them, but studies show they are much more healthier with than without.

This association is more of a survival necessity. These anemones are actually toxic and the fish is resistance to it. If being attacked they will get inside these and the attacker might be stung with this actinotoxin.

Also,

  The presence of an anemone is also essential to reproduction of the
  fishes: their eggs are laid beneath the oral disc overhang of the
  anemone, where they are tended by the male.

Source:

Wikipedia on Sea anemone
INTERACTIONS BETWEEN FISH AND SEA ANEMONES
Clownfish and its mutualism relationship with anemones


Do animals demonstrate target practice (i.e., playful accuracy behavior)? Do animals demonstrate any sort of accuracy-motivated play? (please provide examples!)

Consider most human sports and related hobbies. Most share the common goal of hitting a target or being accurate, and in the case of organized sports, points are typically awarded for being accurate. Archery, firearm past times, football, soccer, basketball, hockey, baseball, tennis, billiards, bowling, darts, beer pong, horseshoes, and countless other examples all are based on competitive accuracy.

Humans seem to be obsessed with accuracy in our competitive past-times. Examination of more ancient sport interests demonstrate less preoccupation with accuracy (though of course there is variation between cultures -- see here or here, ), and perhaps just more with demonstrations of strength and dominance. However, competitive accuracy was alive and well in ancient times: boxing, sword fighting, lacrosse, hoop rolling, golf (and Chinese equivalent Chuiwan), and others already listed are just a few examples of accuracy games with more ancient origins. It seems, then, that the human species has  had a fascination with accuracy for a long time.

However, do animals have the same (or really any) preoccupation with accuracy? I've seen countless examples of animals 'playing' or competing (e.g., pets & captive animals playing with toys & enrichment objects,  young males of various taxa sparring or wrestling, whales playing with their food, monkeys sheep herding on dogs, etc.), but is there any evidence or example of wild animals playing 'games' based on accuracy?

One example that comes to mind is archer fish. There is evidence that they improve with practice, but they practice on targets that are food items, so I'm not sure whether that counts as practice with respect to your question. Interestingly, there's also some evidence that they can improve their accuracy simply by watching other archer fish succeed.


Estimating RPM to RCF in Methods from Older Papers I'm attempting to replicate a cell biology method from a 1958 Laboratory Investigation paper. The protocol is for the isolation of an extracellular matrix protein, and a key step is a centrifugation carried out for 2 hours at 2300 rpm. Apparently it was not common practice to list make, model, and rotor size of centrifuges, so I am a little lost as to what settings to use on my own centrifuge to get the same rcf.

Are there any good starting points for estimating the proper settings? e.g. who the major centrifuge suppliers were at the time or what models would be seen as 'standard' for a cell biology lab?

I am not sure about what they used in 1958 (perhaps Sorvall). However you may look at recent papers for ECM protein isolation (if that was your objective).
Have a look at this article.
From materials and methods:

ECM protein isolation.
Fibroblasts or A431 cells were removed from the
surface of the culture plate with 2 mM EDTA in PBS for 3–5 min at
37⁰C. Detached cells were discarded, and remaining ECM proteins
attached to the surface of culture plates were washed with the same
solution. Cell removal was controlled under the microscope. After
cells were completely removed, matrix proteins were covered with 5%
acetic acid and incubated at 4⁰C overnight. Then, acetic acid was
removed and exchanged with a buffer containing 125 mM Tris-HCl, pH
6.8, 0.1% SDS, 10% glycerol, 1% DDT, 0.05 mM PMSF, protease inhibitor cocktail (Roche, Germany), and incubated at 37⁰C for 1 h. Proteins
were removed with a scraper. The procedure was repeated three times.
All protein extracts, including acetic acid, were combined and ECM
proteins were precipitated by five volumes of acetone. After
incubation at –20⁰C overnight and centrifugation at 7000 g for 15 min,
the protein pellets were dissolved in an appropriate buffer for
further analysis by one- or two-dimensional gel electrophoresis.
In addition, we obtained a Triton X-100-soluble fraction of ECM
proteins. Cells were removed as described above; dishes were filled
with 1% Triton X-100 and incubated at 37⁰C for 30 min. The extraction
was repeated three times. The following procedure of ECM extraction
was the same as described above. Samples obtained from both fractions
were dissolved in a buffer for one-dimensional (Laemmli) or
two-dimensional (rehydration buffer containing 8 M urea, 2% CHAPS, 20
mM DDT, 0.1% Triton X-100) electrophoresis. Proteins that remained
after Triton X-100 extraction were dissolved in Laemmli sample buffer.


How does cartilage become bone? It's a famous fact that bones begin as cartilage and later become bone, but I never was clear how exactly
 this changeover occurs. Could someone please explain this to me?

The process is called endochondral ossification.

It is important to point out that not all bone is derived from cartilage. For example, when a bone is fractured and is healing, the new bone does not always come from cartilage, rather intramembranous ossification occurs. There are therefore multiple mechanisms at a microscopic level by which bone may form. Additionally, bone formation in the long bones is different to that in, for example, the flat bones of the skull.


How does a smoker's finger or mustache get yellowish by nicotine? Tobacco use is the leading cause of preventable death around the world.$\ce{^1}$

The stain is considered as a "tell-tale" sign for identifying smokers. Multiple materials stated that it's due to tar (nicotine) disposition. The colouring fades away after the smoker quits. There are also number of search results that point to "removing" these smoking stains in the skin. If it can be removed using chemicals then I wonder what sort of a chemical it utilized there as well.

Is it only nicotine that causes the yellow stains on the skin? What is the role of oxygen deprivation in this scenario? Can this be categorized under smoker's melanosis? What tissues/cells are being "transformed" in this case? What's the biochemical explanation behind the colouring of skin?

How is this staining differe from a ink stain in the skin which lasts for about about 3-4 days?

Pure nicotine is a yellow colored liquid (although some sources say it's a clear liquid.) "Tar" is a complex sludge that is also yellow-brown. So it's difficult to distinguish 'nicotine stain' from a 'tar stain' based on visual inspection. Let's go to other considerations.

The concept of a 'stain' implies that simple hand washing doesn't remove the coloration. Since nicotine is water miscible, one would expect it's easily removed with soap and water. That implies that either a) a smoker's stain is not primarily nicotine, or b) the nicotine reacts with the skin to create the stain.

Nicotine is sufficiently functionalized that it could conceivably undergo some interesting chemical reactions with proteins, but I don't think that's what's happening. A simple observation is that transdermal nicotine patches do not contain a colored agent, and do not stain the skin. Score one point for the "mostly tar" explanation. Cigarette smoke contains far more tar than nicotine, and tar will deposit on most-any surface (at ambient temperatures), so it's parsimonious to proceed with the "mostly tar" explanation.

The picture shows that the stain occurs on both fingernails and skin. The most abundant protein that's common to those two tissues is keratin. Like other examples of protein staining, the mechanism is complicated and poorly understood, but the basic outline is that parts of keratin are greasy (the non-polar amino acids) that associate with other greasy things.  (EDIT: AliceD's answer also depicts the well-known staining of teeth, which are not keratinized, showing that the staining mechanism is likely a nonspecific adsorption of greasy things onto surfaces.)

The stain can be fixed through the involvement of free radicals and other reactive species in cigarette smoke, like formaldehyde. In this sense, reactive oxygen species are active participants. I don't think oxygen deprivation plays a role here. I don't think this can be described as a melanosis, as the skin isn't producing melanin in response to smoking but is simply being coated in tar.

Even if the stain was completely fixed, the coloring would fade away as the exterior skin cells are sloughed off, consistent with normal skin physiology. This is the explanation for the fading of any stained epidermis. The persistence of tar stains on teeth (which do not exfoliate) further evinces that the stain is removed through the replacement of skin cells.


What type of Bacteria? I did some tests to a bacteria colony and I observed the following:

First of all let's start from the shape and after that we move on to the chemical tests that I did to them:

Form: Circular
Colour: Yellow-to-white (something like pale yellow)
Margin: Entire
Elevation: Flat

Chemical results:

Gram: Negative
Catalase: Positive
Oxidase: Positive

After some research to the databases, I figured out that it might be:

If it belongs to the family of Pseudomonas:

Chryseomonas luteola OR Pseudomonas luteola group Ve-1 with a chance of 48.21%
Flavimonas oryzihabitans group Ve-2 with a chance of 48.21%
Xanthomonas maltophilia OR Pseudomonas-like spp, with a extremely low possibility of 1.34%.

So, my question has 3 parts:

Can someone please tell me if my hypothesis is right?
And if it is possible which bacteria from the above is the correct?
If you manage to find the correct type of bacteria can someone tell me the ideal enviroment to study them better? (agar plates, temperature, time needed, etc.) Thank you for all the efforts made!

Important notice: I have used a blood agar plate with a concentration of 5–10%. It contains as far I know, mammalian blood maybe from sheep or horse. I forgot to check the temperature, but I don't think that it is very important.

Consolidating my comments, and taking all the results at face value (though microbiology can be very tricky), the most likely candidates are Moraxella, or Neisseria spp.
Gram negative cocci (spherical cells) rules out a large number of possibilities, leaving just the above 2 and Veillonella as candidates.

The OP said that the culturing was done under aerobic conditions at 30˚C. Veillonella is an obligate anaerobe, and so wouldn't survive this. Both Moraxella and Neisseria are happiest at 37˚C but would no doubt grow at 30. Both are cultivable on blood agar. Neisseria is best cultured in a 5% CO2 atmosphere, so is probably somewhat less likely. Both appear as pale-whitish colonies on plates. The OP's observation of yellowish colouring could be artifactual of the plate colouring, I'm not 100% sure.
Both are positive for oxidase and catalase.
Neisseria on blood agar:

Moraxella on blood agar:

One final comment: both of these are pathogens, so continue with all due caution.
Moraxella, in particular, is a respiratory pathogen, so I would advise working in a biosafety cabinet. I'll assume you already have the relevant paperwork/permission to be handling > BSL1 organisms...


In what ways can mechanisms of apoptosis be damaged? How many ways can an Apoptosis mechanism be made disfunctional or irreparably damaged? If a cell has damaged Apoptosis mechanisms and it divides will its daughter cells have such damage?

Lot's of ways. Apoptosis is complex, but falls under two pathways ending up at caspase 3. Anywhere in the pathway may there be a problem but also in things that trigger the pathway. For example in cancer there is loss of tumour suppressors which ensure a damaged cell undergoes apoptosis or prevents replication and oncogenes which allow controlled replication. Damage to these genes allows a cell to divide in the absence of signals to divide and also forget to check that it's DNA isn't damaged before replicating. This is then passed on to the daughter cancer cells. As each check is removed the cell permits more and more mutations meaning more and more likelihood for the next mutation to occur. Cancer is caused literally by one cell having defects and every daughter cell also possess the defects. Those that have defects which accidentally kill the cell are selected out.


External "lungs" that process your blood the same as your real lungs do - would that stop your need for breathing? So say your blood goes with a tube out of your body. In an external device all the chemical/biological magic would happen and it would be fed back to your body.
Of course this doesn't exist (yet), but if this would be possible - would it mean you automatically stop your need for breathing?
Is "gasping for air" linked to the amount of oxygen in your blood? Or is there something else going on?
Just a random (theoretical) shower thought. The idea that you wouldn't feel the need to breath feels weird to me.

A device that fits your description does seem to exist, namely an ECMO machine that delivers extracorporeal membrane oxygenation (Fig.1 ). It is defined as:

[A] machine [that] pumps blood from the patient’s body to an artificial lung (oxygenator) that adds oxygen to it and removes
carbon dioxide. Thus, it replaces the function of the person’s own
lungs. The ECMO machine then sends the blood back to the patient
via a pump with the same force as the heart, replacing its function.

The response of patients to ECMO appears to be variable (Crotti et al., 2017):

As the physiologic cardiorespiratory variability is increased in this condition, the dynamic interaction between patient respiratory activity and extracorporeal system function affects the clinical management. The effect of extracorporeal CO2 removal on patient respiratory drive is variable and not always predictable, with some patients responding to CO2 removal with a decrease in respiratory rate and effort and other patients demonstrating a persistently high work of breathing independent on CO2 unload.

Breathing and undoubtedly the exaggerated gasping for air after heave exercise is related to the concentration of CO2 in the blood that's monitored by the brain. Those chemoreceptors basically measure the pH of the blood. However, pulmonary pH receptors exist and a multitude of other physiological mechanisms are at play to keep the level of O2 in check . I happily refer to Brinkman et al. (2020) for an overview on O2 and CO2 homeostasis.

Fig.1. ECMO. source: University of Iowa
References
- Brinkman et al., StatPearl
- Crotti et al., J Thorac Dis. 2018 Mar; 10(Suppl 5): S661–S669


Do mutated c-sis oncogenes only affect cell growth? Since c-sis regulates only cell growth, a mutation there should only lead to an out of control growth of the cell, but the cells would still be mature, since c-sis does not regulate the function or maturing of the cell.

However a mutation in c-sis leads to cancer, and cancer is not just cells that grow out of control, but also don't performe their function (are not mature). Can someone explain how a c-sis mutation still leads to cancer please?

Cancer is not a disease like the flu or E. bola, where there is a single quick and easy cause for the disease which you can locate and describe in a single sentence.  Cancer consists of malignant cell growth, it is true, but why are the cells growing out of control?
The fact is that there is not one single cause.  At some point along the way, some cell experience a mutation to some gene which resulted in a slightly higher rate of proliferation than normal.  However, this in and of itself is not even enough to produce a tumour.  It simply gives the cells a higher number of daughter cells, and consequently, a higher risk of having more mutations.
At some point, one of those daughter cells acquires a mutation which results in higher levels yet of proliferation, or a mutation which encourages angiogenesis, or (in the case of epithelial cells, for instance) a mutation which allows the cell to escape typical anoikis pathways and perhaps perforate its basement membrane without dying.
Even the process of metastasis requires multiple mutations to happen, and yet if a tumour does not metastasize, it is typically regarded as benign.  The point is, cancer is not caused by a single mutation to an oncogene or otherwise.  It is caused by an accumulation of mutations which permit the cells to proliferate much faster than normal, to recruit the body's resources, and to live in tissues all around the body.
In the case of the particular gene that you mentioned, the exact role of the c-sis oncogene in cancer prevention is still unclear; in fact, according to the OMIM page,

The protein product of the c-sis gene has not been identified.

...though the gene is very similar to platelet derived growth factor genes, some of which have been identified as mitogenic factors.  Theoretically, therefore, it is possible that a mutation to the c-sis results in excessive mitogenic stimulation, resulting in an increase in cell division and proliferation.  But that last sentence is speculation, not hard science.
TL; DR:
We don't know, but it's possible c-sis encourages faster cell division.

Sources:

Platelet-derived growth factor, beta polypeptide; PDGFB on OMIM.org
Josephs SF, Guo C, Ratner L, Wong-Staal F. 1984. Human-proto-oncogene nucleotide sequences corresponding to the transforming region of simian sarcoma virus. Science 223(4635): 487-491.


What actually happens to the human body during fasting/starvation? I recently came across a UN study which advocated that controlled fasting can be beneficial for the the human body and I am fascinated by stories of wilderness survival against the odds.

It piqued my interest to ask; what exactly happens to a human body during fasting and ultimately starvation?

I understand that there is a period of glycogen use/exhaustion and functioning becomes impaired but what medically happens to the human body (organs, muscles, protein, body fat, cognitive processes etc) and over what timeline (24 hours to death).  I read that halitosis is an interesting side-effect etc.

Assume the human body has ample access to water and can avoid dehydration.

Actually, the body goes into the fasting state about eight hours or so after the last meal, usually when the guy finishes absorbing nutrients from the food.
Normally, body glucose, which is stored in your liver and muscles, is your main source of energy. When in a fasting state, your body uses up the glucose that you have stored to provide energy. If you are still fasting after this store is used up, your body will start to burn fat to create energy, therefore leading to weight loss.
After fasting for a few days, there will be a higher level of endorphin in your blood which will cause you to be more alert and, weirdly, giving you a feeling of mental well being.
Eventually, if you are starved for too long, your body will start to break down muscle protein in order to create energy (that is why, during WWII, most POW's held by the Japanese were very thin - they were starved and in order to survive, their bodies had to 'eat' their own muscle)
Technically, starvation is when your body starts to eat your protein, i.e. Muscle.During starvation, your body will thin out, because your fat has been burned and your muscle is being 'eaten'. This obviously leads to weakness.
When your fat is being burned, you go through a detoxification process which is caused because any toxins stored in your body's fat are dissolved and removed from the body.
Your kidneys are very efficient in being able to maintain the body's water and salts, like potassium and sodium. But these can be lost through perspiration.
This eventually leads to dehydration which does many things to your body, like: not allowing for your body to regulate body temperature; your heart works harder (most of your water is in your blood (about %$60$) and when you lose the water, your heart has to 'catch' up and pump more to keep the blood flowing and cooling you down - now, your heart is working harder which could give you a greater risk of heat exhaustion); you can feel cranky, drowsy, confused, forgetful.
These are a lot of things that happen when your body is deprived of what it needs in terms of food and liquid.

This is what happens, and this is very general, when your body is in its starvation mode. I am sure that there are many more things, but I could only give a brief answer.


Why doesn't the polar side of the plasma membrane block nonpolar diffusion? It is often stated that small molecules or nonpolar molecules can diffuse through the plasma membrane because they can pass through the middle nonpolar bit, but why don't the polar sides block these nonpolar molecules. Estrogen is nonpolar and can diffuse across the membrane right? Why don't the polar heads of the phospholipids block it? Or look at H+. H+ can't diffuse across the membrane because it's charged (it's not like nonpolar molecule have a repulsive force against it, neutral objects don't repel charged ones as far as I am aware, I don't get why we say polar and nonpolar repel each other, as I understand they just stick to themselves better than each other). Regardless, H+ a small charged molecule would be able to get past the hydrophilic heads right? Estrogen wouldn't be. Where am I going wrong here?
Thanks!

Polar and nonpolar molecules don't actually "repel", it's that polar molecules attract each other much more than nonpolar molecules attract anything. Therefore, to take a polar molecule from the (polar) water on one side of the membrane and bury it in the nonpolar region in the middle of the membrane is difficult because it means breaking its relatively strong interactions with the polar water molecules without forming new strong interactions to compensate.
In the case of a nonpolar molecule passing through the membrane, it is already in water when it approaches the membrane, and transferring it past the polar head groups isn't much "worse" (there's likely a slight effect of the often charged head groups attracting ions that bridge them to one another, but this would be small). The large effect of it being nonpolar, however, is to make it less unfavorable to move it into the middle layer of the membrane where there aren't polar groups for it to interact with.


Is olfaction same among different individuals? For instance if I smell the fragrance of a rose, well it smells like roses (little bit sweet).  But is that smell the same for other people?

Because we also have different voices, why not have different olfaction.

Humans generally have the same set up of olfactory receptors, since they are encoded by genes (there likely are minor differences between people, since there are a lot of these genes). Therefore chemically or physically  all humans can smell the same substances.
However, how a smell is perceived depends also a lot on how the brain reacts to a certain smell (or rather the activation of certain olfactory neurons). Therefore individual people can perceive the same chemical substance a different way - how different depends probably strongly on previous experiences.


Are all chromosomes equally susceptible to mutation? The humans have been around for a few million years, other organisms longer yet. Changes that occur in the genome and propagate (may) eventually throw a new species ... or atleast branch off the old one. Are there any chromosomes out there that may be more susceptible to mutation than their neighbours?

terdon is spot on with the recombination hotspot comment. Mutations are often associated with recombination (information gets lost during crossing-over, so DNA repair is necessary, which of course can introduce mistakes/mutations). It's a fact that there areas in certain chromosomes where recombination happens much more often than other areas of the chromosome. So it follows that chromosomes with more hotspots would likely have higher mutation rates than other chromosomes, on average. This does raise the point, though, that perhaps it's not the mutation rate of the entire chromosome that matters-maybe mutation rates at a more-local level (such as near a hotspot or far away from a hotspot) are more worthy of consideration for your question.
Also, I imagine that sex chromosomes have much lower levels of polymorphism than autosomes. This doesn't have to be because of a lower mutation rate, though: another explanation would be that deleterious recessive mutations on the X chromosome would be purged more easily than on autosomes because their phenotype appears in males (who don't have a second allele because they don't have another X chromosome, so the deleterious phenotype can't be "hidden" like it would in a heterozygote).


Insect identification - Oregon Western Cascade forest, in a small clearing in the grasses. Possibly related to leafhoppers? Looks a little bit similar, and it was able to jump quite well. The last pair of legs are arranged the same exact way as leafhoppers. Assuming it's within Hemiptera. I've never seen one before.

Possibly related to leafhoppers? .. Assuming it's within Hemiptera.

Your assumptions are correct! This insect is related to leafhoppers, in that it's a planthopper, and, is of the order Hemiptera -- it belongs to the species Scolops sulcipes.

According to the College of Agriculture & Natural Resources at the University of Delaware, this is one of eight species in Oregon that belong to the Dictyopharidae family. (source)


Identification of Bioluminescent Species in South Carolina Marshlands I was in the brackish marshlands in South Carolina and the water was lit with short flashes of greenish bioluminescent light from a species that seemed to be floating in the current.  The lights seemed to be associated with a crackling noise as well but I'm not 100% sure that the light and sound were related as there were so many flashes going off at a given.

When I turned a flashlight on I saw some quarter inch long bugs moving in the water but the light was too bright to confirm that the bioluminescent light was coming from those bugs.

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


At what cancer stage do tumors release circulating tumor cells into the blood? And would a very accurate sensitive system for detecting circulating tumor cells (which detects 1 cell per 50 billion) be useful as a screening tool ?

Tumour cells can also metastasise using the lymphatic system. They first need to detach (produce enzymes that break down the extracellular matrix or any adherent molecules etc). Then they need to survive in the blood which is really hard with all the mechanical stress of being pushed around, the completely different nutrients, the different levels of blood gases, the immune cells in the blood and numerous filter mechanisms, then to truly metastasise they need to settle down somewhere and grow in their new environment. That's a lot of things right? So a sensitive assay like one you describe would need to have that tumour cell in the sample (unlikely, and only one cell is required to make a new tumour), is likely to be unable to tell that the cell is a tumour cell, wouldn't be able to differentiate between tumour cells that could or couldn't survive in the blood or differentiate those that could then go on to grow more in a tissue or not. And of course you're missing the entire lymphatic system. Following all of that, why does it matter? See a cancer, cut it out if you can and give chemotherapy to get rid of any possible cells outside of what you cut. If your assay came back negative or positive, treatment wouldn't change.


why male penis not considered as cartilage? Penis don't have bone like ears & nose, then why why male penis not considered as cartilage?

en.wikipedia.org/wiki/Cartilage

feel the tip of your nose. Mush it around, It's got a certain stale gummy bear feeling to it. Now feel your ears, all over. The outer edge, the back, the hard part in the front where the ear meets the face. Feel your adam's apple. This is cartilege.

When you feel your penis, does anything even feel close? Nope. It's just soft. Soft tissue, to be precise.

When stimulated, there are comparmemts within the penis which engorge with blood.

When they fill up with blood, the penis gets hard. That's all there is to it. No bones, no cartelidge.

If you have any questions, noe's the time to ask.


What's the rationale behind freezing one's eggs if cells can be cloned? It seems to me there's a lot of discussions around the topic of somebody freezing her eggs.

What I don't understand though are the following:

Why would you freeze your eggs when you know that the technology for transforming a somatic cell into an egg today exists, or doesn't it see here?
Is it proven that freezing doesn't alter biological activity and hence not diminish the chance of giving birth to a malformed child?

To me it seems way easier and safer (and less expensive) to artificially produce female gametes than freezing them and, 10 years later, unfreeze and hope for them to be still biologically active.

Why Would You Freeze Your Eggs?

For 1, a woman may wish to freeze her eggs if she needs to delay childbirth. This page explores several reasons why, for example, "Women who want or need to delay childbearing in order to pursue educational, career or other personal goals.". Additionally, it explores some basic explanations of the process, if you are interested. If a woman has doubts about her fertility in 10 years time (using your final sentence as an example), such as if she is recently diagnosed with cancer, or needs to finish education but is ready to be committed to having a baby in more than 9 months' time, then she may decide to freeze her eggs for a time when she is more suited to have a baby, using a time when her body is more suited to producing eggs.

Does Freezing Have Adverse Effects?

As for your second question, the same page does mention successfully freezing an embryo for 10 years at -196 degrees Celsius, with no adverse effects on the eventual birth.

Regardless, exploring the risks reveals that the decision on whether the practice is seen as positive or negative is still on the fence - different parties argue for different opinions, as there appears to be no objective truth about proven adverse affects.

The risks described by this clinic are worth considering, albeit minimal compared to a risk of malformed children, however, it is still a popular choice, albeit put forward as 'experimental'. This study (2010, Rudick et al) showed how, in the US, cryopreservation was already being offered in 283 of 442 fertility clinics surveyed. 1/3 of the reasons for the choice was for women with cancer, and the other 2/3 was for women with 'advancing maternal age'.

The ACOG (American College of Obstetricians and Gynecologists), in 2013, stated that they do not endorse freezing of eggs 'for the sole purpose of circumventing reproductive aging in healthy women', however, the ASRM (American Society for Reproductive Medicine) lifted its label as being 'experimental' in 2012. The previously linked article describes a study conducted by the ASRM, which 'reviewed data from four randomized controlled trials and various observational studies that compared fertilization rates, embryo implantation rates and pregnancy rates of fresh eggs versus eggs that were frozen', and 'showed no increase in birth defects, developmental disorders or chromosomal abnormalities when in vitro fertilization cycles were conducted with frozen eggs, leading the society to declare the technique effective and safe'.

Conclusion

Your question is a slightly broad one, and can be answered by the subjective choice of the woman/women involved, however the ASRM still stresses that "we should proceed cautiously in using this as an elective technique", by making a clear line between 'need' and 'want'. However, there is no evidence to show that rates of abnormality are any higher using this method, but considering it is still a fairly new practice that is being marketed as a choice rather than a medical treatment, there is skepticism in the air around whether marketing scientific and medical designs as a mere 'choice' for older women will lead to this technology becoming better or worse.

Additionally, about your comment of it being 'less expensive', this website shows that the average cost of in vitro fertilization in the U.S. is currently about 10,000 - 20,000 USD, whereas the first website I linked (here) estimates the cost at about 10,000 USD to undergo an egg freezing cycle. Although, the prices will change from clinic to clinic. Regardless, the prices are still similar, and the choice lies in the woman choosing to pay and freeze her eggs if, for example, she has recently been diagnosed with cancer, or fears she will not be fertile in 5+ years time.

I hope this answer has been sufficient in answering your questions, and if you have any more questions, feel free to ask me :)

Sources:

http://uscfertility.org/egg-freezing-faqs/
http://www.mayoclinic.org/tests-procedures/egg-
http://www.sciencedirect.com/science/article/pii/S0015028210008009
http://www.ncbi.nlm.nih.gov/pubmed/24463693
http://edition.cnn.com/2012/10/19/health/egg-freezing/
http://www.advancedfertility.com/fertility-treatment-costs.htm


Telomeres in cloning experiments In whole animal cloning ( eg. Dolly ) the nucleus is taken from a somatic cell. So isn't shortening of telomeres a problem ?

Yes, it is. Dolly died of cancer in early years. Length of the telomeres depends on the donor tissue: "In Dolly's study, the animal produced from fetal tissue appeared to have telomere lengths non-distinguishable from normal controls, while the other two, including Dolly, which originated from adult cells, were found to have shorter telomeres." (Xu & Yang, 2003) This statement doesn't mean that embryonic cells are the only cells able to maintain telomere length.

This also doesn't mean, that offspring of animals cloned from nuclei with shorter telomeres, inherits this shortedness: Miyashita et al, 2011

The Xu & Yang, 2003 review is pretty old, you can find newer articles on the topic.


What forms the human amniotic sac? I am trying to understand the formation of embryonic disc for human and chick so the following question is related to here about formation of embryonic disc.

I had thought that the amniotic sac forms only from embryonic disc in humans, particularly of lateral mesoderm and ectoderm of embryonic disc. However, my thought seems to be wrong as my professor says that amnion form only for birds from embryonic disc, but from many different parts besides of embryonic disc for human.

What, besides the embryonic disc, forms the human amniotic sac?

In humans, the amnion (amniotic sac) persists from the primitive amniotic cavity1.  One side of this is formed from the cytoblast (a prismatic epithelium) and the plasmodioblast.  Together these two layers are the ectoplacenta or chorion.  They are also referred to as Rauber's layer.  These replace the lining epithelium of the uterus, whereupon internal cells undergo atrophy to create the amniotic sac.2

The other side of the amniotic sac is formed of the epiblast/ectoderm (internally) and the hypoblast (externally).  Within the epiblast the other layer is comprised of prismatic cells whereas the inner layer are flattened (the hypoblast/entoderm).  This double layer forms the bilaminar blastodermic membrane.2

I'd really reccomend that you borrow the referenced books from your university library as I found the diagrams much easier to understand than the text.

1 Gray, Henry. "Embryology: Formation of Membranes." Ed. Robert Howden. Anatomy Descriptive and Surgical. Ed. T. P. Pick. 15th ed. London: Chancellor, 1994. 90. Print. Colloquially Gray's Anatomy

2 Gray, Henry. "Embryology: The Ovum." Anatomy Descriptive and Surgical. Ed. T. P. Pick and Robert Howden. 15th ed. London: Chancellor, 1994. 82-83. Print. Colloquially Gray's Anatomy


Why replication collapse but not stall leads to DNA break? I have been looking into the concept of replication dynamics and was wondering why collapsing but not stalling leads to a DNA break.

Stalling precedes collapsing. And collapsing precedes breaking. Hence, both stalling and collapsing precede, and lead to, breaking; but not every stalling leads to collapsing, and not every collapsing leads to breaking.


Do Red blood cells(mammals) really have no organelles? I have read that mammal mature Red blood cells lack most organelles, including mitochondria, golgi apparatus and an ER. ( https://en.wikipedia.org/wiki/Red_blood_cell#Mammalian_erythrocytes ) This makes sense since there purpose is to transport oxygen via hemoglobin, and according to the wiki, they make any energy needed via glycolysis. But are there really no more organelles in a mature red blood cells? A simple google search did not help me.

Yes. This is true. During the final stages of red blood cell formation in the bone marrow, the nucleus and several other organelles are broken down and/or expelled from the cells. In the process they decrease markedly in size, from about 24 to about 7-9 micrometer. Presumably this makes them small enough to pass through the smallest capillaries. Lacking those organelles also limits their life expectancy to approximately 120 days.


Why are there exactly 207 morpho-electrical types of neurons? I'm taking an introductory neuroscience course online, and it mentions that of the 55 morphological types and the 11 electrical types, there are 207 morpho-electrical types.  How does this work?  55 times 11 is 605, so it's not a simple mapping of 1 to 1. 207 isn't a factor of and doesn't share any proper divisors with 605, but it's roughly 1/3 (but not exactly). I don't see how a third makes sense though.

What causes exactly 207 morpho-electrical types?

Feel free to let me know if I should move this to Health or Psychology.SE, I'm not quite sure where to post this.

This is just that one author's opinion - it is telling that both sources you have for the number come from the same author. Henry Markram has a leadership role in the Blue Brain Project, a project to create a very detailed computer simulation of a chunk of neocortex to answer various questions. In the context of this project, it is somewhat necessary to make some decisions about numbers of cell types so that they can be incorporated in the model. People can bicker all day long about which types are actually unique types, though.

As far as the mathematics of having 55 morphological types and 11 electrical types, yet only 207 morpho-electrical types rather than 605, the answer is that the matrix is sparse. To get 605 types, you would need to observe all 11 electrical types within each of the 55 morphological categories. If not every electrical type is observed for a given morphological type, you will have less than 605 total. In some cases morphological types are specifically associated with particular electrical types.

You should also read about the concept of lumpers and splitters - in summary, in any context of classification without clear distinctions, different people will come up with different boundaries. It isn't really possible to argue "right" versus "wrong" in this context, because doing so requires weighting different values. Lumping may be beneficial for the sake of simplicity and generalization but miss some details; splitting may allow for more nuance but also risks not seeing "the forest for the trees."


Stretching and compressing bones The Young's modulus of elasticity when a bone is stretched is : 16×109 and when it is compressed, it is 9×109 N/m2. That means, change in length will be more if you compress a bone as compared to stretching it.

What is the biomechanical reason behind this ?

Citing your source would help to answer.

In order to test an elastic modulus, you need to apply some non-zero strain. If the strain is infinitesimal, then compression and stretch modulus will be equal. But if it is finite, then there can be a difference due to the structure of the material.

In bone, I believe porosity will provide most of the dissymetry between compression and extension: at small scales, the material can rearrange using the pores without much deformation. Whereas in extension, there has to be some deformation of the osteons.

In other living tissue, the difference can be due to filamentous proteins: if you compress them, they buckle (form loops) without much resistance. If you exert extensive stress, once they are stretched tight they will resist any further extension. (Think of what a piece of string would do, it's very similar)


How is the "fine mapping of pelvic regulatory region" done in this paper? Could anyone please explain to be in very basic terms how Fig 2, and the associated text(located above the figure) is done? The jargon is too much for me to understand and I really need a simplified, step by step, version of the process to aid my understanding.

Here is a copy and paste of the text, the figure, and the figure description in that order from the paper:

"Fine mapping of pelvic regulatory region. To further localize the position of the cis-acting changes, we looked for the smallest chromosome region co-segregating with bilateral absence of pelvic structures in a cross between pelvic-complete [Japanese marine (JAMA) and pelvic-reduced (PAXB) fish (13)]. High-resolution mapping identified a 124-kb minimal interval, containing only the Pitx1 and Histone 2A (H2AFY) genes, which showed perfect concordance between PAXB alleles and absence of the pelvis (fig. S1A).

Recombination in natural populations can also be used to narrow the size of regions controlling polymorphic traits in sticklebacks (18). We therefore tested whether markers in the Pitx1 region were associated with the presence or absence of pelvic structures in lakes with dimorphic stickleback forms: benthic and limnetic sticklebacks from Paxton Lake, British Columbia (PAXB/PAXL), and pelvic-complete and pelvic-reduced sticklebacks from Wallace Lake, Alaska (WALR/WALC) (fig. S2) (13, 14). Microsatellite markers located in an intergenic region approximately 30 kb upstream of Pitx1 showed highly significant allele frequency differences in fish with contrasting pelvic phenoytpes (P < 10−35) (Fig. S1B and table S2). In contrast, markers around thePitx1 and H2AFY coding regions showed little or no differentiation above background levels. These results suggest that an approximately 23-kb intergenic region upstream of Pitx1 controls pelvic development. This region is conserved among zebrafish and other teleosts (Fig. 2A), suggesting that it may contain ancestrally conserved regulatory enhancers."

http://scienceintheclassroom.org/sites/default/files/stickleback_2.jpg

"Fig. 2.  (A) VISTA/mLAGAN (http://genome.lbl.gov/vista/) alignment ofPitx1 candidate region from pelvic-complete stickleback (SALR), medaka, and zebrafish. Red peaks indicate >40% sequence identity in 20-bp sliding windows; grey bars at topindicate repetitive sequences; and circles indicate microsatellite markers used in association mapping in fig. S1. (B) Reporter gene expression in transgenic animals. (C) Pel-2.5-kbSALR from a marine population drives tissue-specific EGFP (green) expression in the developing pelvic bud ofSwarup stage-32 larvae (36). (F) Detail of (C). (D and G)Altered Pel-Δ2.5-kbPAXB sequence from pelvic-reduced PAXB stickleback fails to drive pelvic EGFP expression. (E and H) A smaller fragment from marine fish, Pel-501-bpSALR, also drives EGFP expression in the developing pelvic bud of multiple stage-30 larvae. This region is completely missing in PAXB."

Source :http://scienceintheclassroom.org/research-papers/what-pelvis-can-teach-us-about-evolution/university

Paper:Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer.  Chan et al.

I'll try to help clarify the picture, but given that I have not read the paper, I am not too clear on the context.

A. IT compares the DNA of the stickleback (the SALR), medaka, and zebrafish. If there is a red peak, there is relatively high sequence identity (or similarity), indicating similarity (in evolutionary ancestry in this context?). Gray is repeating sequence, perhaps due to duplication or some kind of evolutionary history. For microsatellite markers, I believe that the paper is referring to the use of microsatellites (small tandem nucleotide repeats) as markers to compare the three.

B. Reporter genes are expressed and help the researcher identify something (by giving information, such as fluorescence etc.) (eGFP indicates green fluorescent protein e= enhanced)

C-H. These are just pictures of the fishes. Note the fluorescence (green). It indicates some expression (of the gene of interest). The absence or presence of the fluorescence indicates something, based on what the eGFP was attached to.

Hope this helped! But you need to do the analysis yourself, or at least I can't :P


Why do we squint when tasting very sour things? Sometimes while tasting a very sour thing (like tamarind, lemon etc.) our eyes squint immediately and involuntarily for a second, but a little later becomes normal again.

Why, and how, does this reflexive movement occur?

Short answer
Adverse stimuli in general are accompanied by contraction of facial muscles. It is part of our repertoire of emotional expressions.

Background
A disgusted expression and the expression of pain are both accompanied by squinting. Disgusting stimuli include your example of a sour taste, but also include other adverse tastes (bitter) or visual stimuli such as a gross-looking objects. In other words, squinting is likely a common way of expressing adverse stimuli. So the "sour look" may not be easily explained on its own. Instead, it is part of a huge emotional expressive repertoire that makes us human beings. To be able to read these expressions allows us to be empathetic towards others. People with autism and Asperger's syndrome may not be able to do so and are disadvantaged in their social behaviors.

To illustrate the commonalities between sour (#1), disgust (#2) and pain (#3) I would like to share the following web finds.

Sour taste. Source: Getty Images

!
Disgust. Source: Berkeley Emotional IQ test

Pain. Source: Berkeley Emotional IQ test

PS: I am not a psychologist - Consider my contribution as an educated guess.


How potent is the venom from the Australian platypus? The Australian platypus, is a marsupial with a unique feature - in that the males of the species have venom sacs around their hind-claws.

My understanding is that this venom is not lethal to humans, however, how potent is this venom to other animals?

Also, how does the platypus 'manufacture' this venom?

The Internet says that platypus venom can kill small animals, but I haven't come up with a definitive source for this.

There is an informative Wikipedia page about the venom here. Basically the venom contains a number of toxic peptides including a family of C-type natriuretic peptides, some defensin-like peptides and nerve growth factor. Defensins are very widely-distributed in nature but typically are used by cells as antimicrobials. Natriuretic peptides have a range of effects upon fluid balance and blood pressure control - these are the best-characterized components of platypus venom.

These peptides are all genetically-encoded, so they are made as segments of precursor polypeptides. Intriguingly some of the the C-type natriuretic peptides contain a D-Leu residue. (All of the amino acids used in protein synthesis are the L stereoisomeric forms.) The presence of a D-amino acid in a peptide derived from a genetically-encoded molecule suggest that there must be a specific isomerase present, and evidence for this isomerase in the venom has indeed been found as reported in Torres et al. (2006) Mammalian L-to-D-amino-acid-residue isomerase from platypus venom. FEBS Lett.580:1587–1591. The introduction to this article states:

  Platypus venom contains many non-protein and protein components...whose roles are yet to be established.


Which of the two chromosomes in a pair is expressed? I have completely dummy question.

I have 23 pairs of chromosomes in the cells 23 single coming from my mother and 23 single from my father. So how my cell choose which chromosome, mother's or father's to use to synthesize peptides?

The majority of normal autosomal genes have biallelic expression, i.e. the alleles on both chromosomes are used to make protein. This is why mutations in a gene which cause non-function of the product can be silent if the mutation is heterozygous (only found on one of the alleles), because the effect is masked by the second, fully-functional, copy of the gene. In other cases heterozygous mutations may cause slight phenotypes, because half of the protein produced is non-functional.

A small minority of autosomal genes have monoallelic expression, through a process called imprinting. This is where one of the alleles of the gene is modified by methylation of the DNA, or of histones (the proteins which are used to package and condense DNA). This imprinting switches off the expression of that allele, so that protein is only made from the other allele of the gene. Usually in this case, which allele is switched off depends on which parent it came from.

Things are slightly more complicated in the case of genes on X or Y chromosomes. Men have only a single X chromosome, and a single Y chromosome. This means that any mutation on X or Y which causes a phenotype will always present itself, because there is no second copy to mask it.

In the case of women, who have two X chromosomes and no Y, something similar to imprinting happens, where one of the X chromosomes is chosen to be inactivated. This X-inactivation process occurs very early in development, and the inactive X chromosome is kept that way for the rest of that person's life. In this case, however, the choice of which chromosome is inactivated is not dependent on which parent the chromosome came from, and is entirely random.

Some further reading:

http://www.nature.com/scitable/topicpage/monoallelic-expression-8813275

http://www.nature.com/scitable/topicpage/genetic-imprinting-and-x-inactivation-1066


What is the kind of this wasp killing spider from UK? I heard a wasp buzzing rigorously and when I looked at it, it was caught in a spider web. The spider was on top of the wasp. After some time, they become silent. When I exhaled gently on them, spider moved but wasp did not. Later, the wasp was dead. The spider was obviously smaller than the wasp, yet it emerged victorious.

I attached a photo of the spider. While I am not sure whether this is the one killing the wasp, this certainly lives around the event site.

It should be around 1 cm in body length, excluding the legs. It is situated in UK.

Hanging upside-down in a web suggests one of several groups, but in a building structure, and in what appears to be a messy, tangled web, I think we can safely put this one down as a member of the 'cobweb spiders' - the Theridiidae.  This group includes the infamous Black Widows, and some are known to successfully take relatively large and dangerous prey.
So, your particular spider has an obvious clue - the somewhat flattened dark abdomen with a large, light-colored patch in the middle of it.  The shape suggests Steatoda, and there is only one spider that this could be:  Steatoda nobilis, one of several spiders that frequently get called "False Widows".
Here are two links and a representative photo:
https://www.naturespot.org.uk/species/steatoda-nobilis
https://www.cabi.org/isc/datasheet/119917

Oh, I should add that despite the breathless hype the tabloids like to get up to, these spiders are known to be pretty harmless to people.  On rare occasions, a bite (which is not easy to get from these shy spiders) may produce symptoms like a mild Widow bite, but the discomfort seems to pass within a day or so.


How Incomplete dominance can be explained at molecular level? What is exactly happening at the molecular level when two alleles constitute incomplete dominance? Whether the protein formed from each of the alleles constitute a new protein having a different function or anything happens at the RNA level of the two alleles.

Molecular mechanisms of incomplete dominance (a.k.a. partial- or semi-dominance) vary.  As an example, let's look at snapdragons and morning glories, two flowering plants that both exhibit incomplete dominance relative to flower pigmentation.
Snapdragons (Antirrhinum majus) have multiple alleles at the nivea locus.  The wild-type nivea transcript (niv+) encodes a chalcone synthase involved in pigment biosynthesis, and a single copy of the niv+ allele is sufficient for wild-type pigmentation.  However, niv+ is semi-dominant with the mutant niv-525 allele, leading to reduced pigmentation in the heterozygote.  The original publication by Coen and Carpenter 1 describing this effect offers some possible molecular explanations:

Transcription factor sequestration.  The niv-525 allele could encode a defective enzyme.  This allele also contains an inverted duplication of a transcription factor binding domain required for enzyme expression.  The defective niv-525 allele therefore titrates away transcription factor from niv+, leading to less enzyme and therefore less pigment.

Transvection.  There is some physical interaction between alleles on homologous chromosomes, such that transcription of one or both alleles is activated or repressed in trans.  This could be realized as binding of the enhancer associated with the wild-type allele to the promoter of the defective allele.  Figure 9 of Gohl et al. 2 has a good explanatory graphic.

Anti-sense hybridization.  The inverted duplication on the niv-525 allele contains a TATA box.  Transcription initiated at this site would result in a transcript anti-sense to the wild-type mRNA.  Hybridization of the sense and anti-sense
RNAs creates dsRNA that is selectively degraded and/or inefficiently transported out of the nucleus, ultimately leading to less enzyme product.

Morning glories (Ipomoea purpurea) show similar genetics at the A locus, which also encodes a chalcone synthase.  However, unlike the snapdragon niv+ allele, a single copy of the wild-type a allele is not sufficient to produce wild-type pigmentation.  Therefore, incomplete dominance in morning glory results from a simple dosage-dependent mechanism, as described in Johzuka-Hisatomi et al. 3
Citations

Coen ES, Carpenter R. A semi-dominant allele, niv-525, acts in trans to inhibit expression of its wild-type homologue in Antirrhinum majus. EMBO J. 1988;7(4):877-883.
Gohl D, Müller M, Pirrotta V, Affolter M, Schedl P. Enhancer blocking and transvection at the Drosophila apterous locus. Genetics. 2008;178(1):127-143.
Johzuka-Hisatomi Y, Noguchi H, Iida S. The molecular basis of incomplete dominance at the A locus of CHS-D in the common morning glory, Ipomoea purpurea. J Plant Res. 2011;124(2):299-304.


Why high quality DNA should be between 10 and 20 kb? On this website, they are saying that, when using a gel electrophoresis to assess DNA quality, :

  High quality genomic DNA should give a major band of 10-20 kb on the
  gel.

Why is that so? I thought it could be because of the size of the chromosomes, but chromosome X in humans is 156,040,895 bp, which is far from 10-20kb. So why is that threshold of 10-20kb? Is DNA breaking usually in chunks with that size?

The website specifically talks about DNA samples intended for sequencing. The DNA in these samples was/is/will be extracted from cells and this extraction procedure leads to fragmentation (breaking into chunks). Since the expected average chunk length will greatly depend on the extraction process, I guess its reasonable to assume that 10-20kb can be expected from the most common protocols.

Much larger or much smaller fragments will also cause problems with the sequencing. (This is again method dependent, but generally true with varying fragments sizes that can be sequenced with the different available methods)


Do antibiotics attenuate immune response on subsequent exposure to same bacteria? A healthy immune response to a bacterial infection includes "memory" to permit the body to thwart subsequent exposure to same bacteria.  What are the dynamics of using antibiotics on initial exposure to the bacteria regarding a possible degradation of the quality of this "memory" and thus the body's possibly compromised ability to fight a repeat exposure to same bacteria ?

I am not speaking of vaccines ... focus here is on bacteria

A quick search on ISI Web of Knowledge yielded this paper:

  R J North, P A Berche and M F Newborg (1981) Immunologic consequences of antibiotic-induced abridgement of bacterial infection: effect on generation and loss of protective T cells and level of immunologic memory. Journal of Immunology 127: 342-346

The authors investigated the effects of ampicillin treatement in mice infected with Listeria monocytogenes. They reported an abridgement of T cell-mediated antibacterial immunity and in particular an effect upon the development of memory:

  Moreover, Ampicillin-induced abridgement of infection, either before or at the time of peak primary response, resulted in the expression of greatly reduced levels of immunologic memory at a later time. This indicates that memory cells are generated throughout the entire course of the primary anti-Listeria response, including the period of its decay.

Presumably any treatment that reduces the need for an immune response will have an effect upon the production of useful memory T cells.


How do cells determine RNA types? I was reading about the different types of RNA polymerases, and I am confused as to how a cell determines which type of RNA it is transcribing.

According to this nature article:

  RNA pol I transcribes ribosomal RNAs (rRNAs), RNA pol II transcribes RNAs that will become messenger RNAs (mRNAs) and also small regulatory RNAs, and RNA pol III transcribes small RNAs such as transfer RNAs (tRNAs)

The system as to how the different types of RNA polymerase are selected makes sense to me, the core promoter's sequence determines the affinity of the polymerase to itself.

But, how does RNA polymerase II determine if the transcript is a regulatory RNA or a messenger RNA? Can someone explain that process to me or point me to where I would find it?

Another question: When RNA polymerases I and III transcribe their RNA, what prevents the cell from processing them the same way as mRNA and sending it off to a ribosome with a poly-a tail?

Well remember that an mRNA, the RNA that is destined for the ribosome, has already been processed by the time it gets there. This is done by the splicing machinery, among other things (capping enzymes, for example). But the splicing machinery isn't smart in itself. Rather, the gene has the elements, just like it does to select the RNA Pol it needs, to direct the sort of modification the RNA needs to obtain. The image below depicts two types of RNA transcribed by RNA Pol II and how the processing elements let the modification machinery know how to handle them:

Source