text:
Why do marine animals have fins?
Why do Marine animals have fins.

Do you mean fish or marine mammals?  I guess it doesn't matter - they both have fins because selection gave the ones with fins huge advantages in their marine environment.

Welcome to the site! You'll get better answers (and generate more interest) if you can provide a bit more context to your question!

Wikipedia has a pretty decent article on fins which seems to answer your question.

Not all marine animals have fins some have flippers like Sea turtles. Flippers are also present in Dolphins.

It is more efficient to use fins than feet, hooves, or other similar body parts. It is the same reason that you can swim faster while wearing flippers. Having a larger surface area allows animals to push against more water, so that they have more force when swimming. Here is a picture of the bones in a dolphin fin. They are extremely similar to the bones in a hand, because dolphins evolved from land animals that had individual fingers.
Amphibians like frogs and salamanders have webbed feet, which is a "compromise" between feet and fins. These feet allow them to push against water with more power, since they have webbing instead is separate fingers. It also allows them to grip the ground on land, since their fingers can move independently of each other.

Dorsal fins also aid in stability. Many marine animals and mammals are fusiform (torpedo-shaped) to reduce drag in the water and make locomotion easier. Without fins for stability, primarily dorsal fins, it would be difficult for animals to orient upright in the water without rolling. The dorsal fin actually increases lateral drag (rolling side to side) to provide this stability. Check out this reference for more information


text:
How does Topoisomerase II inhibition affect cancer cells?

Topoisomerase II poisons represent some of the most important and
  widely prescribed anticancer drugs currently in clinical use. These
  drugs encompass a diverse group of natural and synthetic compounds
  that are commonly used to treat a variety of human malignancies. At
  the present time, six topoisomerase II-targeted anticancer agents are
  approved for use in the United States, and additional drugs are
  prescribed elsewhere in the world. These agents all act as traditional
  topoisomerase II poisons and function primarily by inhibiting
  enzyme-mediated DNA ligation.

Briefly describe what TopoII does and how it works. Explain what "inhibiting enzyme-mediated DNA ligation" means.
My thoughts for the first question are Type II topoisomerases cut both strands of the DNA helix simultaneously in order to manage DNA tangles and
supercoils. They use the hydrolysis of ATP. It changes the linking number of circular DNA by ±2. After the ends are
cut, the ends of the DNA are separated and a second DNA duplex is passed through the break. The cut DNA is re-
ligated. This  allows the enzyme to increase or decrease the linking number of a DNA loop by 2 units.  It also
promotes chromosome disentanglement. Inhibiting enzyme-mediated DNA ligation means that it prevents the enzymes are not allowed to ligate. This is
prevented by not allowing the formation of a phosphodiester bond.
Cancer cells grow much more rapidly than most cells in the body. What would be the consequence of "inhibiting enzyme-mediated DNA ligation" and why might this be particularly deleterious in cancer cells?
I am really unsure on this one.
I have looked at the Wikipedia answers to this question and they are wrong.

Hi Abigail, this looks like a homework question so it would be nice if you posted your thoughts on what you think the answer might be before we talk you through the bits you're struggling with.

Hey I am new to the site! I added my thoughts on the question.

That's fine, you're question is already improved with that edit!

First question:
In general, topoisomerases are enzymes that relieve supercoiling in DNA strands and tangling in chromosomes. Type II topoisomerases is special among eukaryotic topoisomerases, considering they use divalent metal ions and ATP hydrolysis in their active site. The enzyme cuts both strands of the DNA helix simultaneously (double strand break) in order to manage DNA tangles and supercoils. It changes the linking number of circular DNA by ±2. After the ends are cut, the ends of the DNA are separated and a second DNA duplex is passed through the break. The cut DNA is re- ligated. This allows the enzyme to increase or decrease the linking number of a DNA loop by 2 units. Inhibiting enzyme-mediated DNA ligation means that it prevents the enzyme to re-ligate the DNA strand after it is cut. In other words, the prevention of a phosphodeister bond between nucleotides.
Second question:
In normal cells, DNA topoisomerase II plays several vital roles, mainly to relieve DNA tangles and coiling. This is done by generating "transient double strand breaks" in the DNA strand, which can sometimes cause harmful translocations and damage. Damage of this type is linked to certain specific types of leukemia. This intrinsically "harmful" quality of DNA topoisomerase II can be exploited in cancer cells due to their high replication rate . Certain cancer drugs, such as etoposide, act by altering the active site of topoisomerase II, preventing (inhibiting) the enzyme from ligating cleaved DNA molecules, causing permanent DNA breaks (and inhibiting replication). The fast replication rate of cancer cells ensures that there are large amounts of the enzyme present in the cell, increasing the effectiveness of any Topoisomerase II poisons. However, this drug can also act against some other types of tissues with large amounts of Topoisomerase II, such as cardiac tissue. Also, cancer cells are constantly in a growing/replication cycle, so they exhibit large amounts of the isoform Topoisomerase IIa, the type that is most likely to produce permanent and detrimental DNA breaks.
Source:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2647315/

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Why is there a λ⁴ in the spectral overlap integral in FRET calculations
The Förster resonance energy transfer (FRET) spectral overlap integral looks like:
$$
J=\int_{0}^{\infty}\bar{F}_{D}(λ)ε_{A}(λ)λ^4 dλ
$$
Where $λ$ is the wavelength, $\bar{F}_{D}(λ)$ is the normalized fluorescence emission spectrum of the donor(normalized to unity area), and $ε_{A}(λ)$ is the extinction coefficient ($M^{-1} \ cm^{-1}$).
I am not very familiar with resonance energy transfer but was just curious why would a $λ^4$ term be contained in this spectral overlap calculation. The intuitive implication would be that the longer the wavelength, the larger the spectral overlap?

See for example Eq. 12.1 on page 471 in FRET and FLIM Techniques
(Theodorus W. J. Gadella, ed. 2008) or the corresponding  $\omega^{-4}$ in the integrals of Eq. 14.30 of Sect. 14.5.1  in David L. Andrews' Chapter 14: Resonance Energy Transfer: Theoretical Foundations and Developing Applications

I don't know  why the ^4, but think about excitation energy with longer wavelengths...

If you write the integral in terms of dipole strengths the $\omega^{-4}$ disappears[1]. Perhaps, look at the relationship between emission spectra and dipole strength to see if that explains the $\omega^{-2}$ per factor.

Why this is such a good question

After finishing teaching at 8pm EDT, it took me about 1 hour to find the answer and 1.5 hours writing this answer and confirming things. The Wikipedia article just gives that formula out of nowhere and cites [17] which is nothing but a table of contents (apparently not containing the string "rster" from Förster anywhere) for a book that I couldn't find online, [18] which is a Google Books preview of a book for which something related to the $\lambda^4$ does appear in Eq. 1.2 of pg 13 but explains nothing about where it came from apart from citations to {61}, which is missing from the Google Books preview, and 81-84 which are all books (unlikely to have a free PDF lying around), and [19] which gives the relevant formula in Eq. 14.1 but with no explanation and not even any citations to say where it came from.
Despite having worked in this field for a while, done my PhD in the general area, and even helped supervise a student whose Masters thesis gives a 5-page derivation of Foerster theory starting from page 30, I couldn't find where the $\lambda^4$ came from (the thesis presents the Foerster rate in a different way, which doesn't involve the $\lambda^4$, and I also looked at the reference in there to this paper on my friend Suggy Jang's generalization of Foerster-Dexter theory but it was done in the same spirit as my student's derivation, which unfortunately doesn't help us today with finding the source of the $\lambda^4$).  I thought I was in luck, because my thorough studying of the field meant that I knew one of the best reviews on the topic (this PDF of a paper by Greg Scholes currently with 1238 citations on Google Scholar), but it turns out he literally just gives the integral on Pg. 62 with no explanation. The textbook by May and Kühn might have the desired explanation, but I couldn't find a copy online. Every single paper and/or article I found online with a title like "Introduction to Foerster Theory" or simply "Foerster Resonance Energy Transfer" gave me nothing (some examples of the better resources I found were this, this, some detailed discussions here, this very interesting article by someone who hung out with Foerster in real life entitled "Förster's resonance excitation transfer theory: not just a formula" but then disappointingly it did indeed give "just a formula" at Eq. 4.
The original 1948 paper by Foerster in German (currently with 9994 citations on Google Scholar) doesn't seem to have anything resembling anything close to "the" desired equation. The only research paper by Foerster mentioned in his Wikipedia article doesn't have the equation either, and the famous 1953 paper (currently with 9977 citations on Google Scholar) by Dexter that earned him a spot in the name "Foerster-Dexter theory" doesn't have $\lambda^4$ or $1/\nu^4$ or $1/\omega^4$ anywhere, although now that I have the answer and double-checked all these articles to make sure I wasn't discrediting anyone, I do see that there's a $1/E^4$ in Eq. 16 but it's not as  close to your equation as what I'm about to show you.
The answer

This 1965 "report" by Foerster actually tells us how he got the $1/\nu^4 = (\lambda /c)^4$ right here:

Basically after 53 pages which largely set the reader up for it, he gets this expression for the transfer rate:

In that equation, you can plug in the following:

which will mean you'll get a factor of $c/\nu = \lambda$ in the numerator coming from the molar decadic excitation coefficient $\varepsilon(\nu)$ and a factor of $(c/\nu)^3 = \lambda^3$ coming from the normalized fluorescence quantum spectrum $f(\nu)$: the two combine together to form $\lambda^4$. Since Foerster tells us that these are "Einstein's well-known expressions" for $\varepsilon(\nu)$ and $f(\nu)$, I assume you don't need help knowing why those are proportional to $\nu$ and $\nu^3$ respectively...

... just kidding, explanations and more references about the Einstein coefficients can be found here and here and you'll see expressions proportional to $\nu$ and others proportional to $\nu^3$ in both of those resources.

I even got out my QM text and skimmed through a few chapters... I didn't find it because physicists don't use those functions (the Einstein coefficients physicists are taught are these [https://en.wikipedia.org/wiki/Einstein_coefficients]) Great detective work!

This is cool! Thank you so much for such clear answer!

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Does age affect the frequency of flatus?
Is there any relation between age and the frequency of flatus? I often have this feeling that older people f*** more often than younger ones. Is this feeling scientifically correct?

Hi :) Medical questions here should be explaining how a treatment works rather than what it would be so I removed your last point :)

I do not have access to journals, but there is this paper claiming in its abstract that age DOES NOT play a role in flatus frequency.
Reference:  Furne JK, Levitt MD. 1996. Factors influencing frequency of flatus emission by healthy subjects. Digestive diseases and sciences 41: 1631–5.

Could be that age has an effect. As humans age three important factors, with respect to this question, change:

Diet.
Immune system flexibility and its response to even minor disturbances and infections.
Gut microbiota composition.

This seems to be going on the right track. Could you expand and maybe reference some studies? For instance, how does the gut microbial composition change (and same for the diet)?

I really can't take the time to reference any studies because these are easily found by searching the proper repositories. I have to spend my efforts analyzing our microbiome data to see how that is affected by diet - some very interesting results need to be published. Knowing what to look for should be enough assistance to Shyam to succeed in this quest.

Thanks @Larry_Parnell. I have posted an answer with a link to a paper on this.

@Larry_Parnell: no problems if you do not have time to reference it (I absolutely understand), but then this should be a comment rather than an answer.

Agree this is really a comment.

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Organ cloning - possible to make a non-antigenic organ?
From a J. Neil Schulman article on Organ Cloning:

Cannibalizing organs from other people also entails the risk of
  rejection because of incompatibilities, not only for tissue-typing but
  also for gross anatomical mismatches. Cloning organs [...] has the
  potential of taking a human being's own genetic material and growing
  perfect replacement organs which are fully compatible with their
  genetic makeup.

The reason for using a person's own DNA, is obviously to avoid an allergic reaction to the antigen markers on a strange organ. But in the blood typing system, there exist types which don't have any trouble-making antigens (such as type O-negative, called a "Universal Donor").

Would it be possible to grow an analogous "universal" internal organ, which didn't have any antigens indicating it was a foreign body? (By editing a DNA sample to remove certain expressed proteins, then growing it into an organ.)

I realize this is technically a science-fiction question :) But - A: it may not be in the near future, and B: I can rephrase it to remove the SF component:
In the blood-typing system, the AB antigens don't appear necessary for proper functioning of red blood cells - are the antigens on a person's own cells, actually needed for any essential functions, or could they be removed, without affecting that person's health?

Would this perhaps satisfy your criteria? ~  Could bone marrow transplants be used to prevent tissue rejection of trans-species organs?

@Pelinore that's interesting, but still doing something differently. More like using drugs to reduce an immune-response. I was asking if the organs could be designed to not have an immune response. The linked method would be specific to one person, whereas no-response organs would be generic, and usable by anyone.

"I was asking if the organs could be designed to not have an immune response" Yup, while my one asks if the patient could be designed to not have an immune response :) I think mine might be easier to achieve (if it wasn't for those darn kids! ~ meaning ethics committees of course).

I'll contradict the answer posted here (ages ago) and say no, it isn't possible. Growing an organ wthout MHC proteins might be achievable, but it would be rejected for not having MHC1. NK cells instruct all cells without MHC1 to perform apoptosis. In this case, MHC1 antigens are required on cells for proper self-identification.
Keeping MHC1-less cells alive could be achieved by

equipping them with whatever is keeping erythrocytes and thrombocytes (also lacking MHC1) from being destroyed on sight. (A good idea, but see next paragraph)
disabling their apoptosis mechanism (Cells with disabled apoptosis mechanisms are commonly referred to as cancer, so we might want to not do this.)

MHC1 also has a function; it presents "peptide shreddings" from proteosomes to T cells; this way T cells can check if the cell contains internal foreign proteins (sign of a virus infection or cancerous transformation). Thus, removing MHC from the cells would make them very liable to become nearly unstoppable virus factories or tumor cells.
(On a side note, while everyone technically can receive 0 Rh negative blood, group-identical blood is used always, except in rare emergency cases. A and B antigens here, as far as I know, do not have function.)

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Is there any difference in terms of personal healthcare between complete DNA sequencing and SNPs genotyping?
There are several companies (most notably 23andMe) providing SNP genotyping for individuals claiming that there is no sense for individual in obtaining full genome sequence since only small part of it could be interpreted.
While this agrees with my understanding of the subject, I wonder whether there could be any use to perform full sequence of one's genome for means of personal health care?
The only effect I recall which affects individual's health and could not be caught by SNP genotyping is DNA methylation, but complete sequencing procedure does not detect it either, as far as I know.

Our group does Whole Exome Sequencing. While not as exhaustive as whole genome sequencing, it does offer more coverage than SNP genotyping and can provide more useful data.

Not my field, but I guess most DNA methylation and other epigenetic modifications would be organ specific. I wonder if a buccal swab could give useful information in this context.

If that were true, why do scientific projects bother with sequencing then? It’s way more expensive, and in general most labs don’t have money to waste.

Sequencing gives the researcher data on rare or private mutations that are not on the genotyping arrays.

This difference would have the greatest impact on treatment for cancer, in which a treatment protocol is based on genes deleted, amplified, altered in the tumor vs the reference genome for that patient.
In terms of health risks based on SNP genotypes, the data are far from complete. Sure, some level of risk can be assigned to a variant (SNP), say at certain markers within the FTO gene and risk of obesity. However, the complete list of risk alleles for this and numerous other complex traits is not fully described. Furthermore, the impact of environmental factors (EF), or lifestyle choices, on those genetic variants is only beginning to gain wider attention. For example, a risk allele may not show itself as risk until the EF, such as amount of physical activity or percent energy from dietary polyunsaturated fat, passes a certain threshold. Such gene-environment interactions are thought to contribute to the variance in traits (phenotypes), but to what degree is not known.
Added in edit 15 May 2012: Epistasis, or gene-gene interactions, also are important but far from being cataloged for humans. A situation could arise where one allele elevates risk for a certain condition, but compensatory alleles elsewhere in the genome decrease that risk. We don't know the full extent of epistasis in humans.
Thus, in terms of personal healthcare outside of something like cancer and monogenetic disorders, there may be little that is gained from genotyping or complete genome sequencing, little that is compared to other advice you already know. I carry risk alleles for certain conditions, but there is not really any advice one can give me that is specific for those alleles that I have, where that advice is different than or goes beyond general advice health care providers already have dispensed.

Genotyping only tests for SNPs in predetermined locations. If you have SNPs in other places in your genome, genotyping won't tell you that, but whole genome sequencing will (by comparing your genome to a reference genome available at NCBI). Also, there are other variants such as copy number variations, repeats, insertions and deletions that genotyping can not capture, but all of those can contribute to disease.


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What is the fastest but not venomous snake?
Is it known which non-venomous snake can attack most quickly? I guess it is a snake that attacks its opponent by bites, and not some kind of constrictor.

black mamba (?)

@WYSIWYG Its venomous.

ohh okay.. I missed it... sorry..

The fastest non venomous snake is arguably the Eastern Coachwhip with a top speed of upto 10 mph (reference). If it feels cornered, it will attack with bites but otherwise, it prefers to flee.


text:
Is there a Reverse Transcription optimization for long, 9kb, transcripts?
Has anyone optimized RT for long transcripts (9kb)? The downstream application will be PCR amplification and Illumina library prep.  It will be trivial to make internal primers sets for the PCR that are specific as long as there are no chimeric sequences.  If there are, they will probably get primed also.  If anyone knows of an optimization and/or other potential pitfalls, I would love to hear them.

"Avoiding chimeric sequences" is a good paraphrase of your question (answers don't tell me)? I'd be interested in some basic reference you know of, any link would do.

With longer sequences, the dNTPs become limiting. Try to add more dNTPs while keeping the amount of primer the same. Don't be afraid to run several reactions at different amounts of reagent to find the optimal amount. Also, increase your reaction time. The reverse transcriptase and DNA polymerase need more time to cover a longer transcript.


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What is ischaemia exactly?
I think it is decreased blood supply to organs and tissues.
I also think it is the stopped circulation.
However, both ones cannot be right, I think.
What is ischaemia exactly?

Is insufficient blood supply a better word?

I am asking this because we have too venous congestion which is decreased blood supply to tissue. So Ischemia and Venous congestion should be orthogonal terms.

As I understand it, venous congestion is one of several possible causes for ischeamia. So a venous congestion would lead to ischeamia, but ischeamia does not imply venous congestion.

Ischaemia is lack of sufficient perfusion to a tissue.  Reduced perfusion could therefore mean decreased blood supply to organs and tissues and could also mean a complete cessation of blood flow to an area - therefore both can be correct as they are on a continuum.  Infarction is tissue death due to hypoxia which can result from ischaemia that is not swiftly resolved.


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Can Listeria monocytogenes endotoxin act as an A-B toxin?
I think no, but I am not sure since Listeria is Gram-positive and probably has lipopolysaccharide (exception among Gram positive bacteria).
Can Listeria monocytogenes' endotoxin act like exotoxin A-B?
(In which component B lets component A inside the cell and component A causes the toxicity.)

Considering great research we did after the answer was accepted, I should add important information about the topic. The old (and accepted) answer follows in "" marks for the sake of clarity.
We found that in spite of the earlier reports, the newest ones failed to find endotoxin-like structure in the Listeria born material. Most academic discussions about the issue say there is no such thing called "listeric endotoxin", thus I gave a right answer to a "compromised" question.
I should say that question is still brilliant because it promoted great research and should be an important source for everyone looking for information about listeric "endotoxin"

Listeria endotoxin is not a protein. Thus, is lacks enzymatic activity
  and acts indirectly by binding to sensitive receptors on macrophages.
  Thus, it can not cause lysis itself.
Considering AB-exotoxins, A-subunit is a protein that has enzymatic
  activity (responsible for toxin action)  and subunit B has no
  enzymatic activity (protein responsible for binding to receptors).
Thus, the answer to your brilliant question is NO, Listeria endotoxin
  cannot act as AB-exotoxin being nonprotein and non enzymatic
  substance.
Also, don't be confused with Listeriolysin O, which is listeria's
  eXotoxin protein which is pore-creating protein.

Just to add some important relevant information to the answer from @Ilan.
There is no evidence for the presence of endotoxin/lipopolysaccharide in Listeria.
There was an early report of the presence of LPS (Wexler & Oppenheim, 1979) but this was contradicted by a later study (Maitra et al., 1986). The endotoxin activity of Gram negative bacteria is strongly associated with the lipid A moiety of the LPS. Lipid A is synthesised from N-acetylglucosamine in a three step pathway encoded by the genes lpxA, lpxC and lpxD. I obtained the sequences for the corresponding E. coli gene products and conducted BLAST searches against the Listeria monocytogenes genome with these results:

lpxA - best hit E=0.11
lpxC - no significant hit
lpxC - best hit E=1e-04
the last hit is to a 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase whereas the E. coli gene encodes a UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase. The similarity in the sequences seems to be because they are both members of a large superfamily of acyltransferases.

I conclude that Listeria monocytogenes does not not synthesise lipid A and therefore has no LPS, and no endotoxin.
Wexler, H., and J. D. Oppenheim. 1979. Isolation, characterization, and biological properties of an endotoxin-like material from the gram-positive organism Listeria monocytogenes. Infect.Immun. 23:845-857.
Maitra, SK et al. (1986) Establishment of beta-hydroxy fatty acids as chemical marker molecules for bacterial endotoxin by gas chromatography-mass spectrometry. Appl. Env. Mic. 52: 510-514

Thank you for the addition! I corrected Ilan's answer accordingly.

I"m away from sources now, but I met sources said endotoxin exists

@ilan I tried pretty hard to find any references, so I'll be interested to see what you found.

No problem, will look for the sources later.

@AlanBoyd I tend to agree that Listeria does not produce endotoxin at all. However, multiple sites and even USMLE examination board state it does produce endotoxin. I found older articles than you did, so at this moment I upvote your answer as important one. Although my answer was right, but the question itself was probably biased and compromised.


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Difference between Cary-Blair and Amies transport media for Staphylococcus and Streptococcus?
I normally use Amies medium, but I today heard that Cary-Blair is also possible.
When should you use Cary-Blair medium?

This site (no connection) states (my emphasis):

Unlike Cary-Blair Medium, which is almost exclusively associated with enteric transport, both Stuart and Amies Medium have been widely used for the transportation of a diverse range of clinical swab samples from sites including the eye, ear, nose, throat, skin, genital tract and wounds.

This is very general. I am interested if there is any advantage of using the other in some circumstances. I think if you use Amies transport medium, you do not need to use Cary-Blair transport medium in most of the cases.

I put this up because it clearly states that Cary-Blair medium is used for enteric samples. Whether you should use it for that purpose is not explained. Presumably the Staphylococcus and Streptococcus you refer to are not samples of that type, so you would use Amies.


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

What is this data called by which you can say that the frequencies of eosinophils and neutrophils increased within airways?
I think sample is first taken from throat and cultivated on some general culture (blood agar).
Then, specimen is looked under microscope.
Similarly done for the sample after vaccine.
Then, visual comparison with identifying visually eosinophils and neutrophils.
Is the conclusion made based on culturing, microscopy and visual sampling by eye?
Mass spectrometry
I am not sure anymore if this technique is useful at all.
Mass spectrometry can give different intensities and masses.
If so, the intensity of the corresponding peaks should be greater after the vaccine.
Can this kind of conclusion be made based on mass spectrometry?
Interesting would be to know the exact spectrum of eosinophils and neutrophils after the vaccine. I think they do not increase proportionally.
The one increases more than the other.

Protein mass spec in the 1960s? In this time Sanger did the first protein sequencing, so I highly doubt that it happened with it. From which paper comes this information or has your textbook linked some reference for that? I would say these are either biopsies which are subsequently stained or swabs that where tested. This is from the "Desk Encyclopedia of General Virology" right?

@Chris Today. Can you make such a test with mass spectrometry? I think yes, but the problem can be the amount of the substance from the cultivated specimen.

I think there are ways, yes.

The original tests where done with blood and then:

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

See table 8 in this paper: "Field evaluation of a respiratory syncytial virus vaccine and a trivalent parainfluenza virus vaccine in a pediatric population." So they measure the eosinophils in the periphery not in the airways.
This article used histologic techniques: "Respiratory syncytial virus disease in infants despite prior administration of antigenic inactivated vaccine." Both articles are from 1969.
Newer studies used micropical techniques and FACS analysis, but these experiments were done with mice: "Respiratory synctial virus infection in BALB/c mice previously immunized with formalin-inactivated virus induces enhanced pulmonary inflammatory response with a predominant Th2-like cytokine pattern."

Thank you for your clear meta-analysis and excellent sources! I asked this question because I am interested in separating differently energetic (number of vacuoles inside and their size) eosinophils and neutrophils from one another in video. In all those publications, we have two stages: 1) initial and 2) shortly after the vaccination. I am interested in what is happening between and after these two stages among granulocytes. Some method which enables me to take samples continuously. I think histology and microscopy of each stage is necessary. Then processing pictures and making t-f plane.


text:
What does this sentence about toxemia and Clostridium tetani mean?
I know that Cl tetani is not invasive and strictly localised.
I think toxemia means spread in the blood.
I am thinking this sentence

The volume of infected tissue is small, and the disease is almost entirely a toxemia.

Cl tetani has spores.
This suggests me that these spores spread through blood.
They then open and become pathogenic in some tissues where they remain strictly locally (so small area/volume of infected tissue; I think area is better word, since the disease is not invasive) and pathogenic.
How do you understand the quoted sentence about pathogenesis of Cl tetani?

Clostridium tetani produces a protein toxin, tetanospasmin which causes the major symptom of tetanus, namely involuntary muscle spasms. C. tetani is an aerobic species, does not infect the blood, and apparently only produces toxin in anaerobic conditions.
If a pathogenic bacterium propagates through the bloodstream this condition is referred to as bacteraemia. In the case of C. tetani it is the toxin which enters the bloodstream, not the bacteria, hence toxaemia. The bacteria, being anaerobic, are inhibited from spreading through aerobic tissues.


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DNA methylation and genome size
Is there any relationship between DNA methylation as a level of stability to epigenetic states and genome size? For example, it is claimed that DNA methylation is not required for epigenetic stability in Drosophila melanogaster and yeast, both genomes much smaller than mammalian or plant genomes. Could it be that DNA methylation is needed to help activate/repress certain genomic regions on top of other epigenomic marks when the genome is so vast that there is a need for an extra level of marking? Is there any evidence along those lines?

Is there any relationship between DNA methylation as a level of
  stability to epigenetic states and genome size?

I would say yes, because methylation is used to disable genes in differentiated cells. Disabled genes in differentiated cells generally need to stay disabled to maintain normal behavior for the cell type. Larger genomes usually encode more different types of cells.

it is claimed that DNA methylation is not required for epigenetic
  stability in Drosophila melanogaster and yeast, both genomes much
  smaller than mammalian or plant genomes.

According to my book (S377 molecular and cell biology, book 2, p140) Drosphila don't need methylation because they perform transcriptional regulation by persistent chromatin remodelling instead. Yeast being single celled would have less need for this type of control.

Could it be that DNA methylation is needed to help activate/repress certain genomic regions on top of other epigenomic marks when the genome is so vast that there is a need for an extra level of marking?

It is used as a repressor because it inhibits  hydrogen bonding of transcription factors and the like. I have not heard of it functioning as an activator.
There are also other uses for methylation, for example  newly synthesized DNA is hemimethylated - where the parent strand is methylated and the child one not. From this it can be determined which is the parent strand during DNA repair.


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Are there any examples of proteins with no or minimal sequence identity, but highly similar structure?
What are they, and do they share a common ancestor? How far back in evolutionary time must we go to find them?
If none are known, what computational tools might be used to search for such examples?

Your current question ("Are there any examples of proteins with no or minimal sequence identity, but high structural homology?") uses the term "homology" in a wrong way: Homology refers to common ancestry. So "homology" is binary (like being pregnant), and there is no such thing as "structural homology" (or "high homology" etc.). A more exact question would be: "Are there proteins with little sequence similarity but a very similar structure (and do they share a common ancestor)?"

My god, you're right. Apologies for the oversight, and question edited accordingly. Thanks!

The answer is that common folds are discovered in sequences which are completely divergent where essentially no alignment can be found by conventional means.
David Eisenberg's group created profiles based on alignments from known structures which were more sensitive to discovering whether a given protein sequence was related to a given structure, solving what he called the 'inverse folding problem'.  More recently HMMs have been used from raw aligned sequences which are even more sensitive to predicting whether a given protein structural family can be found in a query sequence.  PsiBlast also deserves a mention as a method that builds such a profile on the fly.  It can come back with sequences that are so divergent that they are probably not really related (personal experience).
A classic example of this is hexokinase, an enzyme that phosphorylates sugars - which shows up in single cell eukaryotes and all animals.  When the structure of actin was solved, it proved to have the same core fold as hexokinase.  Actin is one of the most venerable proteins known in eurkaryotes, so this is now called the actin fold.  None of the software mentioned above would detect this relationship. (I just verified this with psiblast).
Its probably not true all the time, but it probably happens a lot that sequences with the same protein fold are so different that they cannot be detected by any of these means.  Most genomes that are sequenced have dozens or hundreds of 'novel genes' - 40% of E coli is still uncharacterized.  Either there are novel folds popping up spontaneously over short evolutionary time frames or the possible sequences for many protein folds is quite large.  My expectation is that a novel protein sequence can emerge with the same fold in quite quickly, especially in bacteria.

These are all helpful answers, but I think this one is most complete. Thanks!

This paper published last year, address the answer for your question, about computational methods, they mention 3 principal algorithms for structural alignment
of proteins:

Structural alignment directly at the level of C atoms.
The second class of algorithms first uses the SSEs (Secondary Structure Elements) to carry out an approximate alignment, and then uses the C atoms.
The final class of algorithms uses geometric hashing.

And finally you could find useful this paper for an example of this kind of analysis with structural analyses of metabolic families.
References:

 Venkateswaran JG, Song B, Kahveci T, Jermaine C. TRIAL: a tool for finding distant structural similarities. IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 8: 819–31.
 Marsden RL, Ranea JAG, Sillero A, Redfern O, Yeats C, Maibaum M, Lee D, Addou S, Reeves GA, Dallman TJ, et al.. 2006. Exploiting protein structure data to explore the evolution of protein function and biological complexity. Philosophical transactions of the Royal Society of London Series B, Biological sciences 361: 425–40.

The group of Andrei Lupas studies this. He argues that the vast majority of folds arose only once, so that proteins that share a fold are homologous, even if their sequences have diverged. See for example this paper: "Evolutionary Relationships of Microbial Aromatic Prenyltransferases" where they show that there are subtle sequence similarities between two protein families of the same fold, arguing for a common ancestor.

An example possibly worth taking a look at is the variable surface glycoprotein of the bloodstream form of Trypanosoma brucei.
Trypanosomes are the causative agent of sleeping sickness, and the entire cell surface is covered by a single glycoprotein called the variable surface glycoprotein, or VSG. (see here for more information)
These parasitic protozoans have the ability to 'fool' the immune response by antigenic variation.  At any one time just a single VSG is expressed on the surface, but (very rarely) a trypanosome may express a different VSG gene product.  Thus if the immune response succeeds in eliminating all trypanosomes expressing VSG-A, but there exists in the population just one parasite which has switched coat, this variant will poliferate as it effectively presents a different antigen to the host's defenses (and a second immune response will result).
There is litte sequence identity between different VSGs but they are homologous (descended from a common ancestor).
The crystal structure of the N-terminal domain of two different VSGs (MITat1.2 and ILTat1.24) have been solved (Blum et al. 1993; Freymann et al., 1993).  Despite the low sequence identity (~16%), the structures are almost identical.
One other very interesting property of all VSGs is that they are covalently anchored to the plasma membrane via a (C-terminus) glycosylphosphatidylinositol anchor (or GPI anchor).
References

Blum, M. L., Down, J. A., Gurnett, A. M., Carrington, M., Turner, M. J., and Wiley, D. C. (1993) Nature 362, 603-609 [pubmed]
Freymann, D., Down, J., Carrington, M., Roditi, I., Turner, M., and Wiley, D. (1990) 2.9 A resolution structure of the N-terminal domain of a variant surface glycoprotein from Trypanosoma brucei.  J. Mol. Biol. 216, 141-160  [Pubmed]

The following reference contains much useful background information, and is free to all.

Chattopadhyay, A, Jones, N.G, Nietlispach,D, Nielsen, P.R., Voorheis, H.P., Mott H.R., Carrington, M. (2005)  Structure of the C-terminal domain from Trypanosoma brucei variant surface glycoprotein MITat1.2. J. Biol. Chem., 280, 7228-7235 [Pubmed] [pdf]


text:
What is an simple way to burn glucose for visible effect?
I want to make a partially working model of the digestive system that could digest complex carbohydrates. My ultimate goal is to be able to cut up some bread, put it into the model, operate it, and eventually see some effect equivelent to glucose being used in a muscle. I obviously have a very limited buget. How could I simulate glucose being burned in some way that has a visible effect?
Edit: I'm specifically looking for some way glucose can be used to achieve some visible effect that makes sense as a metaphor for combustion, without dangerous/expensive chemicals.

why don't you burn it?  the combustion will give off hot gas you can use to drive a piston.  just a thought.  like the handle.

Or put it in a balloon and watch the balloon inflate as the bread is converted to co2 by microbes

But, how would you burn dissolved glucose?

You need to define "burn". In this context, it sounds like a synonym for "oxidize"

You could combine the demonstration that glucose can be burned with the principle of catalysis: a sugar cube won't burn by itself if you hold a match at it. Using a bit of MnO2 or even simple ash on the cube will make it inflammable through catalysis: the MnO2 acts as catalysator (is not used up).
MnO2 (manganese(IV) oxide), a dark powder, is a safe chemical that only reacts with acids, and is insoluble in water.

cool. does this actually work? And is it within the confines of a not expensive or dangerous chemical? I know little about MnO2 other than what I've just learned from Google!

This, however, is probably not what the OP wants, I for certain don't have MnO2 and fire in my digestive system or in my muscles in order to digest sugar...

I have added a bit about MnO2. @nico: but the sugar won't be oxidized without catalysts, i.e. enzymes, and this principle is what the demo is about.


text:
Online course on Plant Taxonomy and Physiology
After following a course in Permaculture, I realised that if I want to get serious about it, I need to be able to distinguish plants. So I am looking for an online Video course on Plant Taxonomy and Physiology. My understanding is that it is a fairly standard course in basic Botany degrees, and since there are more and more school that put their material online it is quite possible that one of them might have placed this online too. Any suggestion?

these are traditionally taught separately, unless the class were to address the relationship between these topics.

What other science courses have you taken? What are your goals? It sounds like a general botany course that touches on these subjects would be a good place to start.

I don't think you're likely to find a good online course in taxonomy - you will be able to find the basics (mentioning mono/dicots and key families). I might make a quick guide as a blog post (but it will have to wait a couple of weeks until I have more time). As for plant physiology, your best best is to read a good text book. I strongly recommend Plant Biology by Smith et al. (2009). Before going into plant physiology you will need a grounding in biology. As David already asked, what's your background?

Thanks for your answers. I have a degree in math, a Master in IT and a PhD in systems biology. Yet none of this was of any use respect to actual recognizing plants. Yes, books can help but I have several books but they never helped much. On this topic (and I stress that on other topics is different) it looks like I absorb more from seeing things than from reading about them.

Well, I wasn't able to find an online video course. The closest I came was this site, which links to courses that put their material online. Most of these are compilations of the lecture notes. There's also this page from the University of British Columbia, that has a nice little overview of the field of plant taxonomy.
In my experience, botany and plant identification are subjects where one really needs to learn by doing. You really need to grab a plant and take a close look at it while noting why its in the group that its in. A great way to get started might be to join a local gardening club or native plant society. The people in those groups can provide their tips for ID-ing plants.
One of the primary skills you'll want to learn is identifying what family a plant is in. Plant families have (mostly) consistent characters, and learning how to spot the most common families in your area will be a big help.

I don't know of video course, but here are two book recommendations:
First, Botany in a Day by Elpel is superb in terms of being an approachable, systematic look at plant identification and basic botanical knowledge.
Second, as I mentioned in this answer, the Botany Coloring Book is a great resource for basic self-education on botany / plant anatomy.


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Why is there an increase of diagnoses of Lyme disease?
On the Center for Disease Control page for Lyme disease, you can see the progression of reported cases of Lyme disease from 2001 until 2016 and see that over time, there are more reported cases of Lyme Disease.

I am wondering if there is an actual increase in incidence or if, perhaps, there is an increased awareness of the disease causing doctors to be more likely to test for it (and diagnose it) than they were in 2001.
Is there any information supporting one or the other?

One of the opinions expressed on the CDC website is that the increase of diagnosis of the Lyme disease could be accounted to expansion of ticks:

Since the late 1990s, the number of reported cases of Lyme disease in the United States has tripled and the number of counties in the northeastern and upper Midwestern United States that are considered high-risk for Lyme disease has increased by more than 300%. One explanation for this trend is that the ticks that can transmit Lyme disease have expanded their geographic range and are now being found in places they weren’t seen 20 years ago. --Rebecca Eisen, Ph.D. (source)

I have also found a report containing another possible explanation:

Areas of patchy woods, which are very common in cities and suburban and rural areas, may have higher populations of Lyme-disease carrying ticks than forest fragments, which generally have fewer species than continuous habitat. This is because some species thrive in smaller places.
White-footed mice, for example, are more abundant in forest fragments in some parts of the country, likely because fewer predators and competitors remain there. These mice are particularly abundant in patches smaller than about five acres, which could spell trouble for people living nearby: the mice are the main carriers of Lyme disease-causing bacteria. In the eastern and central United States, Lyme disease is contracted via blacklegged ticks that feed on infected mice, then transmit the bacteria when the ticks bite people. As a result, says biologist Felicia Keesing of Bard College in Annandale, New York, Lyme disease is concentrated in areas where people live near forests with blacklegged ticks.
Keesing, scientist Richard Ostfeld of the Cary Institute in New York and other researchers found that smaller forest fragments had more infected ticks, which could translate to more Lyme disease. Forest patches that were smaller than three acres had an average of three times as many ticks as did larger fragments, and seven times more infected ticks. As many as 80 percent of the ticks in the smallest patches were infected, the highest rate the scientists have seen. These ticks may also be infected with other emerging diseases--Babesiosis, Anaplasmosis and Powassan encephalitis--therefore, forest fragmentation might also be contributing to other serious illnesses, Ostfeld says.
"Our results suggest that efforts to reduce the risk of Lyme disease should be directed toward decreasing fragmentation of deciduous forests of the northeastern United States, particularly in areas with a high incidence of Lyme disease," says Keesing. "The creation of forest fragments smaller than five acres should especially be avoided."

EDIT: Another article on Vox also provides some possible explanations including the global warming, reforestation of farms and increase in the number of deers (caused by hunting protections).

My understanding is that there is a population increase of ticks, due to the milder winter temperatures.
Testing for Lyme disease is done with a specialized and somewhat expensive procedure called ELISA. Also as the prevalence of lyme disease has increased, physicians have become more aware and are making preliminary diagnosis , based on typical symptoms.
So its a two-part situation, increase in tick populations, and increased sensitivity for making diagnosis.


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Two brown-haired people have two children, P and Q. P has blond hair. Q has brown hair. What is the probability that Q is heterozygous?
Two brown-haired people have two children, P and Q. P has blond hair. We therefore believe that each parent is heterozygous and that blond hair is a recessive trait.
Q has brown hair. What is the probability that Q is heterozygous?
My answer:  2/3.  There are four possibilities Bb, bB, BB,and bb. Before observing the color of Q's hair, we assign equal chance to each.  We eliminate bb as a possibility.  The chance that it is bB or Bb and not BB is 2/3.
A Biology PhD disagrees with me and says that the probability is 1/2. Who is right?

now ask that PhD to solve the Monte hall problem.

@Memming that's http://en.wikipedia.org/wiki/Monty_Hall_problem

I am familiar with the Monty Hall problem.

Assumptions: Blonde hair is Homozygous Recessive and that the traits are strictly Mendelian.
The parental generation must be both heterozygotes as at least one child is Blonde (bb). So your cross is Bb x Bb.
Your square is going to look like this:
           _B_            _b_

_B_         BB           Bb

_b_         bB           bb

So of the question is:

What is the probability that Q is heterozygous?

The PhD is INCORRECT. They probably just made a simple Punnet Square in their head and forgot the caveat that you have to exclude "bb" because Q is not Blonde. The possible allele combinations for non-Blonde offspring from a Heterozygotic cross are only BB, bB, Bb.
Therefor the probability that Q is Heterozygous is indeed 2/3 (bB, Bb).
It's not uncommon for PhD students - who are often deep into their own research - to gloss over details and possibly give incorrect answers because the information hasn't been relevant to them for years (most traits aren't Mendelian, strictly recessive or dominant, and rarely involve a single allele), so give them some slack unless they were being a jerk about it. =)

Just to complete the answer, this essentially is an application of Bayes' theorem

I worked it out that way, too.  But adding another layer of mathematics isn't going to prove anything to someone who disagrees with the simple way of seeing things.

Then you have one more argument: this was probably a high school homework, so it has to use what kids learn about Mendelian heredity, not something deeper and more elaborate.


text:
What does the term 'modified residue position' in phosphorylation mean?
Does it mean the position of the amino acid in the protein sequence, or something else?
For example, I came across the phrase "S 368 phosphoryation" where S is the modified residue and 368 is the modified residue position. What does it all mean?

You are correct, the 368 stands for the position of the amino acid in the protein's sequence - this particular serine is the 368th residue in the protein counting from the amino-terminal end.


text:
vestigial structure question
If a species has a vestigial anatomical
structure that it no longer uses, would
you expect this structure to disappear
over many generations through the action
of natural selection? Always, sometimes,
or never? Explain your answer.
I'm having a hard time with this question. I don't know what should I do

Its a homework question, right? Can you describe your basic ideas or what you understood?

I'm studying for an exam and the professor put this Q on a slide. I can't really remember what he said. I think the answer is Sometime. and there was something about recessive genes involved. Umm, I understand the natural selection concept and whatnot. But I can't gather enough infromation to answer it.

If a species has a vestigial anatomical structure that it no longer uses, it may or may not disapear through natural selection.
Evolution is based on four mechanisms :
- mutation
- natural selection
- sexual selection
- genetic drift
A no longer used structure can disapear if a mutation makes it to. Then, if it confers a selection advantage (natural or sexual), then individuals without that structure will survive and / or reproduce better than the other. The mutation will spread among the population and structure may finally disapear.
If it does not confer benefit the individual nor decrease it's chances of survival or reproduce compare to others, mutation may or may not be conserved and so for the structure.
Genetic drift can accelerate disapearance of a structure, especially if the population is really small, even if it does not confer any advantages to the individuals. The mutation can rapidly spread through the population just by chance.
For example, in human body, the appendix is no longer used but still remains. It's absence does increase chance of survivol nor is attractive to sexual partners, so it doesn't imply natural or sexual selection structure. Genetic drift may or may not randomly make it disapear one day, no one knows.

The appendix is not entirely vestigial.  It's a safe-house for gut flora following a bout of dysentery, and in places where dysentery is common, it  probably saves lives.


text:
Does coloring affect the perception of depth?
I have a question about the mechanics of human vision which may be as much of a physics question as it is a biology/physiology question. I noticed that if I try to imagine a clear blue daytime sky contrasted with a clear night sky and ask myself which of the two appears closer, my intuition says the daytime sky appears closer. My next thought was, given that a night sky is mostly black, visually the only difference between the two skies is their color. So why is that I want to "blue" is closer than "black"? And if the difference in color is truly what produces the difference in perceived depth, can similar effects be noticed with other color pairs at more familiar distance scales?
But then again, there are a couple of alternative explanations that seem more plausible to me on second thought. A black night sky could just as easily be called a dark sky, and the difference in perceived depth is really more a matter of shading. Then I remembered a night sky has stars of course, and it might be that my mind just wants to place the stars at normal "sky depth", forcing the black backdrop to appear even further away.
(Another related question I've been somewhat curious about: what precisely is the perceived "distance to the sky" as far as our intuitions are concerned?)

see Wikipedia http://en.wikipedia.org/wiki/User:Karam91/Chromostereopsis for a starting point

That was very helpful. Good to be able to a name to the effect. Thanks!

Yes, color and shading can certainly affect depth perception, as explained by wikipedia:

Aerial perspective – Due to light scattering by the atmosphere, objects that are a great distance away have lower luminance contrast and lower color saturation. Due to this, images seem blurry the farther they are away from a person's point of view. In computer graphics, this is often called "distance fog." The foreground has high contrast; the background has low contrast. Objects differing only in their contrast with a background appear to be at different depths. The color of distant objects are also shifted toward the blue end of the spectrum (e.g., distant mountains). Some painters, notably Cézanne, employ "warm" pigments (red, yellow and orange) to bring features forward towards the viewer, and "cool" ones (blue, violet, and blue-green) to indicate the part of a form that curves away from the picture plane.

Here are a few examples:

The above is Manet's "Luncheon on the Grass" - and if you look at it briefly it seems the bathing woman is sort of hovering amidst the trio instead of rinsing herself off in the background. This is because the warmer colors flanked by more saturated greens in the grass around her "pull" her forward into the same space as the rest of the painting. Here, scale is one of the major cues that she should be in the background.

Above is Cezanne's "The Bay" and is an excellent example of how warmer colors (reds, yellows, oranges) are used to add depth when contrasted with cool colors (blues, greens, violets). The image works very well, and that's partially because of the colors chosen. You can almost draw a diagonal line between the warm and cool portions of the painting.

I noticed that if I try to imagine a clear blue daytime sky contrasted with a clear night sky and ask myself which of the two appears closer, my intuition says the daytime sky appears closer. My next thought was, given that a night sky is mostly black, visually the only difference between the two skies is their color. So why is that I want to "blue" is closer than "black"?

Well, there are many differences between the two! The daytime sky has numerous reference points - the horizon, mountains, clouds, airplanes, nearby buildings, etc. I would bet the reference points are the number one reason you perceive the daytime sky to be closer, as our brain is constantly taking them into account without us thinking about it. There are other cues, too: The daytime sky has a gradient to it - that is, the blue of the sky differs due to the curve of the atmosphere, and gradients increase depth perception with more saturated colors being perceived as closer (as opposed to the edges of the daytime sky, which are often less saturated).
The night sky, on the other hand, is pretty much solid black (if you live in suburban or urban areas). The lack of a gradient or other colors immediately robs the observer of some depth perception, and because of the inky blackness of night the other reference points - the horizon, nearby structures, airplanes, clouds, etc. - can practically disappear, robbing the observer of additional depth perception.

Thank you MCM. Your response was very helpful, and I feel like it gives me a lot to go on for learning more. Cheers!

I had this same question.  I believe the answer is this is a known effect caused by aberrations between your eyes and the way they perceive color.  This effect is called Chromostereopsis.  I know this is an old topic but hopefully this information will be useful to people like me who were also trying to learn more.
http://en.wikipedia.org/wiki/Chromostereopsis

More information (as opposed to a link, which could rot) would be appreciated.


text:
Shigella's O antigen (PAI synthesised) and passage through host defences
The O antigen is synthesised by Pathology islands (PAI).
O antigen may be a factor why Shigella survives the passage through host defences.
I am interested in which step of pathogenesis.
There are Bacterial ATPase (actin tail, intracellular movement), M-cell (enter) ...-> extracellular movement.
Where can the O antigen affect in Shigella?

The outer layer of the cell envelope of Gram negative bacteria is the outer membrane, and the outer leaflet of that membrane is composed largely of lipopolysaccharide (LPS). The O antigen is the name given to the outer glycan portion of the LPS - there is a nice diagram at the Wikipedia article I have linked to which makes this clear.
Because this structure is exposed at the bacterial surface it is a target for the immune response, and the serotyping of many bacterial species incorporates this O serotype information.
Table 1 of the review that you link to indicates that PAI SHI-O carries genes gtrA,B,V (originally derived from a bacteriophage - not unusual for a pathogenicity island). These genes encode enzymes which modify the O-antigen via a glucosylation reaction. Presumably this helps the bacteria adapt to an immune response via a shift in serotype. It may be, for example, that an invading population of Shigella includes variants which do or do not express these genes so that a subpopulation can arise which is not recognised by an existing immune response. This is what is meant in Table 1 of the article by "evasion of host immune response". It is a common strategy - examples in Salmonella (flagellar phase variation) and Helicobacter (induced transformation) spring to mind.

Do you mean by the induced transformaton of H.pylori the generation of lophotrichous flagella (mucinase) which permits intracellular movement?

No, I mean that under stress conditions, (such as an immune response), when cells ares dying, other cells will take up their DNA (transformation). This results in new variants arising (through recombination) some of which are able to continue the infection.


text:
Knockdown of long noncoding RNA (lncRNA) - how is it done?
I don't work at the wet lab and don't know all the details about the knockdown techniques.
My question is:
How lncRNA knockdown is done?
For example - you have lncRNA that is functional in the nucleus. How is it possible to do knockdown using iRNA if interference happens only in the cytoplasm?
Sorry if there is biology related misconception in my question.

Knockdown of lncRNA in mammals is not done via RNAi. Instead, one transfers antisense DNA oligos which bind to the RNA. This triggers the action of the RNase H enzyme, which degrades RNA-DNA duplexes. It degrades the lncRNA.
UPDATE: For reference, I learned about this from a seminar, and it is not very well documented, but after some literature search I found this paper to quote:

Although we (Fig. 3A) and others (42, 49) have used siRNA to knock down NEAT1 lncRNA and although the knockdown of strictly nuclear RNAs has been well described (53, 54), we remained concerned that because NEAT1 is mostly a nuclear RNA (55), it may not be very efficiently targeted by the RNAi machinery. Nuclear RNAs, however, are proficiently targeted using complementary antisense (AS) oligodeoxynucleotides that recruit nuclear RNase H activity to degrade the RNA (56). Hence, we also employed complementary AS oligodeoxynucleotides to knock down NEAT1 lncRNA in HIV-1 NL4-3-infected Jurkat cells (Fig. 4C, left). The AS approach reduced NEAT1 (Fig. 4C, left) and increased HIV-1 p24 production (Fig. 4C, right), providing results consistent with those from siRNA-mediated knockdown of NEAT1 (Fig. 4A and B).

Reference or it didn't happen :)

I added a reference

Nuclear RNAi happens.. check these articles:
http://www.nature.com/nrg/journal/v14/n2/execsumm/nrg3355.html
http://nar.oxfordjournals.org/content/early/2011/11/07/nar.gkr891.full
Also there is some evidence that Ago2 binds to lncRNAs.
However, you can employ other techniques to knock down lncRNAs for e.g. ribozymes.

This is controversial, but most groups in the field have concluded that RNAi does not work in the nucleus despite the presence of Ago.  When lncRNA have been KD'd with RNAi, they are usually shown to be present in both the nucleus and cytoplasm, and the KD is thought to occur in the cytoplasm, not nucleus.  Of course as always in biology it is possible that nuclear RNAi does occur in some cell types or under some special conditions.  Gapmer oligonucleotides acting via RNAseH are usually an excellent way to KD a nuclear lncRNA, but I would add that you should be prepared to test say 6 or more different oligos, as the efficacy is unpredictable, and in contrast to RNAi, there are no great generally available algorithms for antisense oligo design.


text:
Epistasis Involving Multiple Loci
The following problem is from Schaum's Outlines on Genetics, 5th edition, by Elrod and Stansfield.  I'm having some trouble solving it.  It is found under a section entitled "Interactions with Three or More Factors" in the problems at the end of the chapter on Epistasis.

Problem 4.30 (pg. 112):  If a pure-white onion strain is crossed to a pure-yellow strain, the
  F$_2$ ratio is 12 white : 3 red : 1 yellow.  If another pure-white
  onion is crossed to a pure-red onion, the F$_2$ ratio is 9 red : 3
  yellow : 4 white.  (a)  What percentage of the white F$_2$ from the
  second mating would be homozygous for the yellow allele?  (b)  If the
  white F$_2$ (homozygous for the yellow allele) of part (a) is crossed
  to the pure-white parent of the first mating mentioned at the
  beginning of this problem, determine the F$_1$ and F$_2$ phenotypic
  expectations.

In the first crossing, it looks like the type of interaction is one of dominant epistasis between two loci.  So, we could call the alleles for the first locus W and w and the alleles for the second locus A and a.  Then W-A- and W-aa would have a white phenotype, wwA- would have a red phenotype, and wwaa would have a yellow phenotype.  This would be consistent with the ratios provided in the problem.
In order to explain the 9 red : 3 yellow : 4 white, a third locus can be considered with alleles B and b.  Proceeding as above, where we had the locus for W or w epistatic with respect to the locus for A and a, we could have the same locus for W or w epistatic with respect to the locus for B and b.  This time, wwB- and wwbb would be white, W-B- would be red, and W-bb would be yellow.  This would be consistent with the 9 red : 3 yellow : 4 white ratio.
This is where I get stuck.  If the locus for W and w is epistatic in a dominant way with respect to one locus and in a recessive way with respect to another locus, then all onions would be white.  Therefore, I must have done something wrong.  Am I on the right track?
This isn't really a homework problem, despite the "homework" tag.
Here are the answers provided in the text for the problem:

Problem 4.30 (pg. 115):  (a) 25% (b) F$_1$: all white; F$_2$ : 52
  white : 9 red : 3 yellow

Is it necessary to have atleast one common loci for the two crosses? I fail to see that mentioned in the question.

@SatwikPasani: I've added the answers in the text for the problem to the original question (I apologize, it would have been better to do this when the question was first posted).

After reading Satwik Pasani's comment to the original problem, I tried using the hypostatic locus as the common locus in the epistatic relationships, instead of the locus causing the onions to be white.  The following solution fits the answers supplied in the book.
Three loci can be used to determine the colors of the onion, the alleles of which can be denoted by C, D, and E.  Suppose that C and D are each epistatic to E, such that the phontypes of the onion are given as:
cc---- white
--D--- white
C-ddE- red
C-ddee yellow

Then the first crossing in the problem can be given by CCDDEE x CCddee.  The second crossing could be ccddee x CCddEE.


text:
Features in individuals causing high population variation
As I understand it, a population with high variation is something sought after, since it makes the population better equipped to face a dynamic environment.
Then, I guess features in an individual which causes it's population's variation to be high, should be selected for (high mutation rate, other features.. ?).
If so, does this manifest itself partly as individuals preferring to mate with individuals from another population? (With genetic difference within reason, perhaps a norm for a proffered genetic difference between individuals)

I think you have an interesting question here but I think you are giving too much intent to evolutionary processes.  Unless the population is being managed (like in a preserve or zoo) there is no one to strive for high variation.  In a dynamic environment, a population with high variation is less likely to go extinct but this is not consciously anticipated or planned for by the members of that population in the anthropomorphic sense that you seem to imply.

Assuming a population lives in a highly dynamic environment and mutation is the only source introducing variation. Some in the population has genes that code for a slow mutation rate and the others have has genes that code for a high mutation rate. Shouldn't genes that code for a mutation rate appropriate to the environment be selected for? Perhaps a rate that is proportional to the environment's 'dynamicness' , in this case high.

The term "striving" and the phrase "the individual should strive" raise concerns like those in the comment by @DQdlM. I would suggest re-phrasing the question.

I believe there are evidences in both directions in terms of mechanisms to favor variation in a population: outbreeding and crossing within individuals that look alike. There is a fine line between the two. Outbreeding helps in keeping variation and mixing variants that appeared in different parts of the population, but too much outbreeding can generate inviable offspring. Too much inbreeding also reduces viability. Certain plants have features that are selected to favor outbreeding and make inbreeding incompatible by rejecting incompatible ("self") pollen (self-incompatibility mechanisms).

authors: Атанас Танев


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How selfish is Dictyostelium slug formation?
Dictyostelium is a slime mold which is well known for having a single cell free living phase and other some conditions (e.g. when food is scarce) for forming communal piles of cells called 'slugs' which migrate as a proto animal.  Eventually the slug can turn into a fruiting body with a stem and a nodule of spore forming cells at the top.  The spores can then be carried off by the air and seed dicty further away.
Apart from being amazed at the seeming ability to form amoebic, animal, plant and seed like forms, there must be a lot decision making happening at the formation of the stalk and fruiting node at the top.
So my question is: what is the current thought about how cells compete in the mexican hat and stalk formation to be at the top of the pile?  Its pretty altruistic of the cells in the stalk to do this - some web pages say they die, is that right?  Links to references after 2007 or so would be appreciated unless it's all been decided.
By analogy its always been pretty altruistic of 99% of our bodies to let our gonads reproduce, but we are (approximately) homogeneous genetically.  In the wild is slug formation heterogeneous?  How does genetic diversity influence slug and fruiting body formation?

Yes we're homogeneous genetically and each (well OK, most at any rate) of our individual cells reproduces, just not sexually. I am not sure altruism enters into it for bona fide multicellular organisms. Perhaps we could say the same of dicty? Do the stalk cells also replicate in order to grow the stalk?

That is the theory, but in practice, I think its stickier than that - there is some heterogeneity in the cells of the body.  I doubt there would be any mysterious force that would cause a conflict in the organism if the germline contained a code for some significant genome changes in some of the organs of the developed body.  If there were an advantage to it, it would persist....

Joan Strassman's work is probably the route to go for this.
The short of your answer is that several things mediate who ends up where in the slug:

Cheaters are limited from exploiting other
  clones by high relatedness, kin discrimination, pleiotropy, noble
  resistance, and lottery-like role assignment.

Here's the most relevant paper:
Strassmann, J. E., & Queller, D. C. (2011). Evolution of cooperation and control of cheating in a social microbe. Proceedings of the National Academy of Sciences, 108(Supplement 2), 10855-10862. [pdf]

thanks @Atticus29 Let me take a look and see if this is clear..

The answer appears to be 'not very selfish' as over 90% of slugs found in the wild were all closely related.  Is that right?

The answer to your original question, "So my question is: what is the current thought about how cells compete in the mexican hat and stalk formation to be at the top of the pile? Its pretty altruistic of the cells in the stalk to do this - some web pages say they die, is that right?"
is that the assignment to the spore part is by lottery. It is very altruistic (in the sense that individuals die in the stalk). As you point out, it seems pretty common for individuals to be very closely related (although chimerism seems possible).

well its not really altruistic if they are all closely related.  I think the fraction of others are being selfish, but that ratio they find is usually similar to the amount of selfishness allowed in such systems in the simple simulations I know.  you have got your checkmark sir.


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Mechanism behind Philadelphia chromosome translocation?
I was reading up on causative factors of leukemia on medicinenet and I came across the following statement:

...an exchange between chromosomes 9 and 22 leads to what is known as the Philadelphia chromosome.

What is the mechanism behind this? Is it purely mechanical? Would the locations on both chromosome’s be equidistance from the end (for lack of biology vocabulary.) In other words, would each segment involved in the swap have to be similarly sized?

Hi, in this paper you might find some details: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1762911/
In brief: 1) the mechansims can be several, I wouldn't say "purely mechanical" but it is related to the physical/chemical properties of the region of chromosome involved (some regions have sequences that for partly unknown reasons are more prone to be translocated than others). 2) It is not necessary that the two regions have similar size, and actually unbalanced translocations (in the exchange is not reciprocal) exist.


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How do I prepare and clone from E. coli DNA?
I'm looking for a protocol to get genomic DNA from an E. coli sample so that I can clone a small portion of it using PCR into a plasmid.  (< 500 bp in this case).
It seems OWW (Open Wet Ware) only discusses preparation of fragmented DNA. Does this mean I have to cut it up before I can clone from it?  Any pointers would be really appreciated.

What is OWW? Acronym expansion or a link would be helpful.

It's a wiki for describing consensus protocols and organizing lab webpages: http://openwetware.org

@shigeta could you elaborate on what you mean by cloning?  Do you want to incorporate a fragment of the E. coli genome into a plasmid and then transform the plasmid for cloning?

thanks Mac - edit added Kevin. @ Mac That's right - in this case I want to clone a < 500 bp segment from the genome and pop it into a plasmid like pGLO.

Is anyone still looking for an answer to this? Phenol/chloroform extraction is the gold standard. And here's a protocol specific to E. coli genomic DNA that doesn't use phenol/chloroform: http://bio.classes.ucsc.edu/bio105l/EXERCISES/DNA/genomic.pdf

The answer I got from a colleague is that to PCR from a bacterial sample, you can add bacteria right to the PCR tube without even lysing it.  maybe this so obvious nobody thought to say this....

@shigeta Oh yeah, I do that often when screening colonies following a ligation/transformation. Stick a colony with a toothpick, stir in some water, use the water for PCR. I increase the first 95C step of a PCR protocol from 2 min to 4 min. These reactions aren't the cleanest though - if you amplifying a gene for downstream cloning, I'd still recommend purifying the DNA first.

Hey all I think I didn't know how to word this question properly.  After asking a colleague I was told that I don't need to prepare the DNA at all for this tiny non-library scenario.
She told me to just take a little smear of bacteria on a toothpick and put it into the PCR reaction with the master mix and the enzyme and the heating cycles would do the rest.
Maybe this question was too simple - sorry if it was.
( Sure enough it worked fine.  )

Yes, you must fragment the genome in order to insert it into a vector for cloning; you can't "insert" the whole 5 Mbp genome of E. coli into a vector.  It's difficult to transform cells with huge plasmids, 2-20 kbp is an optimal range.  In any case, if you want a clone of the whole genome, wait 30 minutes and the cell will happily oblige you.
Most procedures that isolate genomic DNA will fragment it in the first place, as it is much too large and fragile to stay together, and if it did it, the majority would be caught up in other cell debris and discarded.  Vortexing with glass beads is a typical first step to randomly fragment it.  After this, you can digest the DNA and your vector to place matching ends on it, ligate it, and transform host cells.
If you want a targeted approach (to extract a specific gene, a technique with which I am unfamiliar), you may be able to use PCR on your extracted, fragmented DNA, as there would hopefully be one intact segment spanning what you want.

To clone a specific gene, you have to design PCR primers that will amplify the gene and also with specific restriction sites flanking your gene. The restriction sites should correspond with the restriction sites found in the poly-linker of your plasmid. For ligation, digest your plasmid, treat with CIP (to reduce vector background), and ligate it with your purified and digested PCR product. Needless to say, this is probably an oversimplified explanation of cloning; let me know if you want more details.

@JamesPan I've subcloned genes between vectors, I just didn't know if there was any differences between vector->vector and genome->vector.  It's all DNA so in theory there isn't anything new, but I don't know about the practical considerations.

i thought cloning meant to PCR a fragment of the genome - i've never head of popping the genome fragments into a plasmid directly - you would have to have a lot of genomic DNA to do this - sounds hard.

@NickT I think genome->vector should still be the same general principle. Amplifying genes from genomic DNA should still be straightforward (I amplify genes from human DNA all the time). I find that sometimes, at least in human DNA, it can get fussy at you, so I try different PCR additives like DMSO or Betanine. Use ~50ng of E. coli genomic DNA for your template, amplify, get your products, and insert it into a vector just like anything else.

@JamesPan feel free to post another answer; your experience and depth of knowledge seems better than mine.  The more answers, the better.

feel like you are telling me how to PCR something off genomic DNA while i am hoping for a protocol to purify the chromosomal DNA in order to copy it by PCR...


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Is this a grackle with an unusually long decurved bill (Phoenix AZ, USA)
Can someone help me identify this bird (sorry only had the iphone)? It looks like a grackle, but the bill is much longer than any I have seen. The bill looks like a Le Conte's thrasher, but it was all black. It looked pretty ratty because he was molting. It was definitely black, and in an area with lots of grackles.
The pictures don't do it justice, it was a really long bill. The pictures were taken in Phoenix, Arizona, US on Greenway bike path near Thomas Rd on 7 Sept 2014.

The picture is not that clear, but it definitely was not something that the bird was holding in his beak. That was my first thought when I saw him, but I watched him awhile, it was very clearly his beak that was long and decurved. Sure wish I had my real camera at the time.

Could it be that the bird was holding something into its beak, which made it look curved?

It could be a crow, a blackbird or a raven for all we know because deformed bills on birds has been a matter of debate (reference) and there is a group on flickr (reference) where you can post such pictures. I have actually noticed few pictures of birds with beaks that resemble the one in your photo.

A crow with a deformed bill (reference)


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Why do people have antibodies against other blood types?
The ABO blood type divides each blood type according to whether they have the "A" and "B" antigen(s) (AB has both, O has none). People also have antibodies against the antigens they don't have (AB has none, O has both), even before they have ever come in contact with those antigens.
Why do people have antibodies against these antigens they have never come in contact with? This isn't the normal situation for the immune system (e.g. for a virus or the blood type rhesus factor)

The only reasonably satisfying exploitation I've ever heard is that human gut flora contains the A and B antigens and thus antibodies are created in a reaction to that. But I've never found satisfying reference material or sources for that explanation.

I am not sure I understand your question fully.  The specific immune system has the potential to make antibodies for lots and lots and lots of antigens it has never come in contact with.  Essentially every time you get a cold it is the specific immune system producing antibodies for an antigen that it had not encountered.  If it had encountered it before, then you would have memory cells and likely wouldn't get sick.  In reality it is amazing that we have so few blood antigens and that we can transfer blood as easily as we do.

@DQdlM The difference is: normally you will not have antibodies for antigens you have not come in contact with. E.g. when first encountering a specific type of influenza you will start making antibodies against it. This is why vaccination works. But blood antibodies are special: you already have antibodies for blood antigens even if you've never come into contact with other blood.

interesting.  So the antibodies are present in the blood even w/o exposure to the antigen?  I always assumed that we just had the potential to make the antibodies if the antigen was encountered.  I will have to look into this a little more.

It is written in "Biology - Campbell and Reece " that development of the antibodies occur due to microbes living in our body having antigens similar to other blood group's antigens.

According to the Wikipedia entry for the ABO blood group system:

Anti-A antibodies are hypothesized to originate from immune response towards influenza virus, whose epitopes are similar enough to the α-D-N-galactosamine on the A glycoprotein to be able to elicit a cross-reaction. Anti-B antibodies are hypothesized to originate from antibodies produced against Gram-negative bacteria, such as E. coli, cross-reacting with the α-D-galactose on the B glycoprotein.

The cited reference is Van Oss, CJ (2004) Letter to the Editor: "Natural versus Regular Antibodies The Protein Journal 23:357, available here. This source contains this statement:

..."we have known for more than four decades that these bloodgroup (antibodies) arise out of minor infections occurring very early in life..."

The cited references are:
Pettenkofer et al. Z. ImmunForsch. 119: 415-429
Springer, GF (1960) Klin. Wschr. 38: 513-514
Unfortunately I have access to neither of these articles, and besides they are presumably written in German.

We each inherit either A, B, AB or no antigens from our parents.
The current thought is that when you're between 0-6 months old you are exposed to bacteria/viruses that contain very similar antigens (A or B). These antigens are similar enough to the A and B antigens found on red blood cells that any antibody created against these bacterial antigens would also react against the corresponding red blood cell antigen. Seeing as you can't produce an antibody against your own antigen (except in rare circumstances), you always produce the opposite antibody to what antigen you have.
I hope some of that makes sense. Feel free to point out any glaring mistakes I've made, wouldn't be the first time! ;-)
Source: I'm a biomedical scientist.

I am posting so long after the initial question as I replied to a more recent similar question that was marked as a duplicate. On being redirected here I was surprised at the answers as the question (and certainly that of the supposed duplicate) did not give any indication that he was aware that the situation for non-compatible blood-group antigens was any different from any other foreign antigens. I think it appropriate, therefore, to append the following (@KennyPeanuts has also commented in this vein) for the benefit of those unfamiliar with the idea of clonal selection.
To put it simply, clonal theory of antibody selection assumes that the antigen-specificity of antibody-producing cells is random, so that all types of specificity will exist. On encountering an antigen a particular cell will be stimulated to divide and hence allow the production of a greater amount of antibody against the antigen.
Immune tolerance requires that cells producing antibody against self antigens be eliminated at some stage. Hence people of blood group O, lacking blood-group antigens A and B, will not have become tolerant to them, and will have antibody-producing cells capable of producing antibodies against them, should they encounter them in an incorrect blood transfusion.

I think your answer does not invalidate the others, but it is a requirement? The existence of A/B antigen specific naive B cells is necessary, but those B cells will not produce antibodies until exposed to the antigens (in the context of an inflammatory response). The above answers argue that the "exposure" comes from infection with pathogens that have antigens similar enough to the A/B antigens as to cause cross-reactivity. So the activated B cells will produce antibodies against the pathogen antigens that also recognize A and/or B antigens in blood cells.

@ddiez — OK. I've modified my answer taking your remarks into account. I still suspect that one of the questioners (the one who posted the supposed duplicate) had no knowledge of the special situation for blood group antigens (I certainly didn't) and that my answer forms a basic introduction which the other answers lack.


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Does a top heavy population grow, decline or stabilize?
Imagine a population that has a larger proportion of older individuals than younger ones, what could possible happen to it in the future?
I am guessing that if the older individuals reproduce, the population will increase but as the older generation grow older they would eventually perish again decreasing the population. As they form the larger proportion, the net population would eventually grow but decline, but would the population then begin to stabilize or continue declining?

Your question leads to the field of structured population models, and I am afraid the answer is: It very much depends on the exact Leslie matrix!. The population may go extinct, may remain at stable size or may grow indefinitely (theoretically speaking), may increase in size and then go extinct, etc…
This is at least true if you make the assumptions that the rates that govern transitions between age/stage classes (survival, growth, reproduction) are  stable over time. Your scenario is explicitly dealing with transitory population dynamics, i.e. it is asking about the population fluctuations that will happen before the age-structured population stabilizes (assuming it does stabilize at some point).
To understand what will happen to your population you can model your population using a Leslie Matrix.
Leslie matrix
The Leslie matrix describes the age-specific survival and fecundity of individuals in a population. Shortly speaking, a population dynamic model using age-specific survival and fecundity looks like this:

Renaming the matrix and the two vectors you see above it gives: $n(t+1) = M \cdot n(t)$, where $n(t)$ is the vector of number of individuals in the population at each age and $L$ is the Leslie matrix, where the first row gives the fecundity of each age ($f_2$ is the fecundity of the individuals of age class $s$ where the number of individuals is a given time is given by $n(t)$) and the lower diagonal gives the survival probability ($s_2$ is the probability of surviving from age 2 to age 3).
So, basically to answer your question, define your Leslie matrix $L$, define $n(0)$ and iterate (left multiply your vector $n(t)$ several times) to see how the number of individuals change through time.
Leslie Matrix and Linear Algebra
The right leading eigenvector of $L$ gives the stationary distribution and the associated eigenvalue gives the growth rate $R$. If $0<R<1$, then the population size decreases through time if $R>1$, the population size increases through time. $R$ cannot be lower than zero (see Perron-Frobenius theorem to understand why). Many biologically interesting features can be extrapolated from the Leslie matrix such as the average lifespan or wether you'd better to introduce individuals of a age 1 or of age 2 (for examples) in a natural population in order to prevent its extinction. The sensitivity of the population to change in parameter (such as an increasing mortality rate at lower age due to a new predator for example). You will find more information on the Leslie matrix on the wiki article and on many other websites.
Other ways to model using a Leslie Matrix
One can also model age-structured population using right matrix multiplication (unlike the above example) and use row vector rather than column vector. The Leslie matrix may also be a function of various variables such as the population size. One can also extend the Leslie matrix to incorporate different class of individuals in the population (different genotypes or different sexes for examples).
Books
Charlesworth (1994) and Caswell (2001) are both excellent books to go deeper into the subject of structured population models, but may be challenging if you lack some background knowledge in linear algebra or population biology.
Hope that helps!

EDIT - R simulation
It's been a time I haven't programmed in R. So, I took the advantage of your question to have some fun and write a quick and dirty code. Below you'll find a R code that allows you to see how the age-specific population size varies depending on your initial vector $n$ and the Leslie matrix. I also add some instructions in order to change the number of age classes (because my code is not very flexible).
install.packages("ggplot2")
require(ggplot2)

######## Parameters

n = c(2,23,40,300) # initial age-specific population size. MNodify as you which. You can as well change the number of age classes

L = matrix(c(0,0,1,2,0.8,0,0,0,0,0.8,0,0,0,0,0.3,0), byrow=T, ncol=4) # Leslie matrix (Left multiplication). Modify as you wish but make sure it should always be a Leslie matrix. You can modify the number of age classes

nb_generations = 100 # Number of generations you want to compute

############

n_t = data.frame(age1=rep(0,nb_generations), age2=rep(0,nb_generations), age3=rep(0,nb_generations), age4=rep(0,nb_generations), Generation=1:nb_generations) # It is a data frame to keep track of age-specific population size changes through times. You will have to add more `ageX` columns if you want to simulate more than age classes

# print (n)
for (generation in 1:nb_generations){
    n_t[generation,1:4] = n
    n = L %*% n
#   print (n)
}

n_t2 = reshape(n_t, direction='long', idvar='Generation', v.names='Age_Specific_Number_of_Individuals', varying=c('age1', 'age2', 'age3', 'age4'), timevar='age') # Just to reshape the data for convenience!

ggplot(n_t2, aes(x=Generation, y=Age_Specific_Number_of_Individuals, color=factor(age))) + geom_line() + scale_color_manual(values=colorRampPalette(c("black", "grey"))(4)) # change the last number of this line according to your number of age classes.

You can see that there are important osciliations in the first 30 or so generations just as expected. Then, the population more or less stabilizes. You also see that due to a survival probability that is different from 1 for each age class, there is necessarily at equilibrium more individuals in age class 1 than in age class 2 and more in age class 2 than in age class 3, etc...

Made some small additions - I hope this was ok.

@fileunderwater You did very well! Thank you!


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What does min mean?
I read that

"trp operon is located at 27 min on E.coli chromosome."

What does "min" mean ?

Min means minutes. Minutes are counted for interruption points since onset of DNA transfer in F-pili-mediated conjugation. The point "0" is not associated with ori, but is close to thr. The total chromosome size is 100 min (time taken for conjugation).
See:

Linkage Map of Escherichia coli K-12, Edition 10: The Traditional Map
Recalibrated linkage map of Escherichia coli K-12

Well.. I am not sure if this 100 minute is for the replication or transfer. I am still confused because this site says it is replication. In fact I did write conjugation first and changed to replication.

in fact replication is much faster in regular conditions.

Yes, 100 min is the time required for the transfer, since replication time itself is ca 40 min.


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Movement of stem cells from mother to fetus
Recent results from J Lee Nelson and colleagues (Sci Am. 2008 Feb;298(2):64-71; available as full text through Google) show that cells from the mother were found in a person aged 46. Logically, these cells should be stem cells, as any other cells would die in such a long period of time.
So, what stem cells could be transferred from mother to fetus?
Why doesn't the immune system reject those cells?

Please add a full reference and link to the paper.

They could also be immune system memory cells, as they are (by necessity) extremely long-lived

Yes, a link to the reference would be most helpful. In the meantime, I found some abstract from a conference where they apparently presented this work here: Chimeric maternal cells as T lymphocyte targets in pediatric SLE

Please don't include articles directly into your posts, firstly it's huge and makes your question pretty much impossible to read but also it's very very close to plagiarism and copyright circumvention.  Usually linking to a pubmed index or the journal itself will suffice along with fairly quoting any relevant sections.

There's a lot more out there on mother-child cell exchange now -
e.g. a nice plain-English explanation of microchimeras from the baby in the mother here. Anyone feel like having a stab at answering this one?

This is also child->mother rather than the opposite, but I was interested to spot that the earliest publication documenting "feto-maternal trafficking" is substantially earlier than 2008 - 1893! (https://www.ncbi.nlm.nih.gov/pubmed/16620961)

The link in the OP is now broken, but it appears to be a reference to this paper by the Nelson group: https://www.nature.com/articles/3700471

Since the maternal cells can be found in a number of tissues including

In second trimester fetuses the thymus, lung, heart, pancreas, liver, spleen, kidney, adrenal gland, ovary, testis and brain had maternal Mc (microchimerism)

it's clear that these are stem or stem like cells that are being incorporated into fetal tissue.
Since these cells arrive while the immune system is developing, they are considered as self and not foreign. But a breakdown of that immune tolerance is thought to be involved in a number of autoimmune diseases, especially systemic sclerosis which resembles a host vs graft disease where the patient's immune system attacks tissues holding the maternal cells.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516290/


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Can ingestion of B6 cause gastrointestinal disturbance?
Can the ingestion of vitamin B6 upset the stomach, and if so by what mechanism?

However, in all cases along these lines, see your doctor rather than the internet :)  There's a lot more to be safely gained through thorough history from a professional and clinical examination than through a question asked on a website

It is not reported anywhere that Vit B6/Pyridoxine has gastrointestinal side effects.


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Why is the blood pressure in the superior vena cava during inhalation less than during the exhalation?
For further investigation into the progress of the blood pressure, we will measure a patient's blood pressure in the superior vena cava measured during inhalation and during an exhalation. His heart function remains the same during the measurements
Why is this subject's blood pressure in the superior vena cava during inhalation less than during the exhalation?

The diaphragm moves down during inspiration. This leads to air being sucked in, due to the pressure difference created. The converse is true during expiration. As the thoracic space is where the SVC sits, it's pressure decreases during inspiration as it is subjected to the surrounding decrease in pressure.