Are genes associated with obesity selected for? I've read that there are several SNPs associated with increased risk of clinical or morbid obesity. I was wondering if there is any evidence that these are under positive selection. Would you expect them to be so?

I guess I'm interested to know if they would previously offered a selective advantage and only recently, say in the post-war period in the West morbid obesity become a problem due to differences in the diet.

Related question:
How many, and how severe, are known single gene polymorphisms for obesity?

This is called the "Thrifty Gene Hypothesis" which was first used to explain why diabetes is so common. Basically it suggests that these alleles would have provided some kind of advantage, over the other possible alleles at that loci, until the environment changed. Then the environment changed and the allele became harmful. Environments are always changing and therefore favour different alleles (variant of a loci).

I suggest the genes linked to obesity in the modern world would, if tested on the old world populations would have been linked to being of a healthy weight. Further, those without it may have been skinnier and more likely to suffer from the disadvantages of being in such condition.

However, this paper present some counter arguments to the thrifty gene hypothesis. Speakman suggests that the genes responsible spread via genetic (allelic) drift rather than by positive selection. It is worth remembering that drift is very poor at spreading new mutations through large populations so there are also weaknesses to his arguments.

One example of a change in the favoured allele caused by an environmental shift is the DDT resistance gene in Drosophila which was present in the population at very low levels for a long period of time. As an aside, it possibly remained this way because it was subject to sexually antagonistic selection - beneficial to females whilst detrimental to males. It then spread through the population when DDT pesticides were used because it obviously became highly beneficial.  Many other examples of environmental change leading to different selection are around, this is just one off the top of my head. Another is the Galapagos Finches in a drought in the late 20th century.

HTH, if not please ask more and if it does then please accept it!


Are all emerging viral diseases of the past 100 years zoonoses? From my basic understanding: The viruses causing Ebola, Sars and Covid-19 are all the result of a zoonosis, meanings that the viruses have passed from animals to humans.

So my question is: Are all recently (let's say 100 years) emerged viral diseases, with potential for a global epidemic, the result of a zoonosis?

To my knowledge, yes. A partial list of recently emerged/emerging viral diseases (I certainly could have missed some), with probable reservoir hosts:

Chikungunya* (birds, rodents)
coronaviruses (SARS [bats], MERS [camels], COVID-19 [?? bats ?? pangolins ??])
Ebola and other filoviruses (Marburg): (bats?)
Hendra, Nipah (bats)
Ross river virus* (various mammals)
HIV (primates)
influenza (H1N1, avian) (birds/pigs)
monkeypox (monkeys, duh; also rodents)
West Nile virus* (birds)
Zika* (? "a wide range of animals in West Africa")

Starred examples are vector-borne (so perhaps of slightly lower concern - might not fit your criterion of "capable of causing a global pandemic").

Omitted:

older zoonotic viruses (rabies, dengue, hepatitis, ...)
non-viral zoonoses (malaria, plague, anthrax)

A list of zoonoses; another from US CDC

More generally, the only other place an emerging virus could come from would be from mutation or recombination of existing human viruses. I'm not aware of such an example.


How does DNA resolve on size exclusion resin? We generally have a good idea of how DNA separates using agarose gel electrophoresis, how well does DNA resolve on a SEC resin like superose? I get the impression that salt influences where it elutes.

Is it possible to compare the molecular weight of DNA and where it elutes to the molecular weight of proteins and peptides and where that elutes?

It works pretty well and can be used to desalt DNA. The DNA runs a bit different than proteins since it is more a long stretched molecule while a lot of proteins are globular. See this references (the first is about the behaviour of DNA on superose):

Size-exclusion chromatography of DNA restriction fragments. Fragment
length determinations and a comparison with the behaviour of proteins
in size-exclusion chromatography.
Size exclusion chromatography of DNA and viruses: properties of
spherical and asymmetric molecules in porous networks
Size exclusion chromatography of plasmid DNA isoforms


Is this a type of fruit fly? I live in Taipei, and these flying insects are about 2-4 millimeters long (body length). They are very active when it's over roughly 24C indoors, and will fly, land and run around randomly on interesting surfaces then fly again, all in one continuous motion.

Some have moved into my apartment again.

They are attracted to food, especially coffee grounds!, vinegar, bread, and dark, moist areas. I can use these attractants to catch them inside bottles or plastic bags, but can't ever seem to get the last one.

I see them fly around while mating end-to-end (twice as long as a single fly) and they often go right past my face while doing so as if to say "ha! there's more of us on the way!"

The heads seem smaller than in images of common fruit flies that I've seen.

Are these likely to be fruit flies, or something else? I don't need an exact species identification, I'd just like have some kind of classification to describe them with besides "little flies".

In this answer to a related but different question, it was proposed that they were something very different, but I don't think that's the case.

Photos: the best I cold do with my cell phone plus a magnifying lens.

I can't pinpoint on the species name but a quick common fruit fly should give you a image which look very similar to the one in your photos.

these Bois are around 1/8 in inches long
-striated abdomen

Hope this is the one


Does becoming martyr have an evolutionary advantage? This is related to
How does "be altruist to those who are similar to you" evolve?

Altruism that is

Not reciprocal
Not familiar

has little explanation. One possible explanation is that the trait itself may correlate well with genetics. One great answer there is that often the cost of altruism is small anyway. It can explain why people vote. Here the expense is small anyway.

Still there seems to be some factors that are even bigger.

Let's take a look at people that die for their ideology. Christian martyrs, Muslim suicide bombers, or Communist guerilla fighters. They seem to get so little and well, die.

And that's pretty common. It seems pretty easy for a leader or pedagogue to rouse men to be soldiers. Of course, becoming a soldier is a pretty shitty job, yet most men don't mind.

These people make a huge sacrifice for the sake of their country, ideology, or people that are not even genetically related to them.

Why?

There isn an effect called "Indirect reciprocity" where individuals just give to everyone they meet without direct requirement of reciprocity.

This sort of benefit to others is common - hospitality to strangers, general politeness, good customer service all fall along these lines.  You hope they will come back and benefit you again, but maybe they will tell someone else who will know you are a good community member.

It is only sustainable in a system where the cost/benefit ratio is less than the reputation benefit of the act.  It sounds as if this is only good for public acts but if the benefit is transferred to a social entity that outlasts the individual (like your children, a relative's children, a religion or a corporation say), the result could still hold.

If you think about typical morality/ethics really it still makes sense to think that what we call altruism must still have a net positive benefit.  If there is no benefit long term or to anyone, it really isn't useful or even good, its random.  What we usually call altruism is usually some sort of reciprocal cooperation.

A soldier who dies in combat or someone who dies for their beliefs but everyone knows about it as a public statement benefits from their act indirectly.  I don't think its altruism in the pure sense of the word. Defending the nation, ones' beliefs or whatever is, in its sense its own reward.  Veterans come back from a war are hopefully respected for their work.  Having a purple heart can be a good thing to show people.  I'm not saying these people are adequately compensated for what they have been through, but just trying to draw a distinction between pure biological altruism and 'indirect reciprocity'.

Examples of Indirect reciprocity might be the use of tax money to build highways and build power and water infrastructure.  Its important - its the glue that holds a nation or a group together.  If you got punished for doing these things we wouldn't be hanging as a nation very long!

A martyr with no family at all who would benefit would still count as an altruism I think, but most acts of public piety and sacrifice do benefit the individual by reputation. Something to think about.


Has synthetic biology created new plants or animals as of 2013? I've seen a Ted.com talk where the speaker suggests that modern science can create new micro organisms, like bacteria with a pre- defined new set of traits. But has anyone create a new species of plants or animals using synthetic DNA yet? If so, what are their names?

Answering your question

Well, considering there is a plethora of facilities that deal with the cloning of plants and animals, as well as altering specific DNA in order to create a better plant or animal. Tests have been done with rats to try and create stronger and smarter rats, and tests have been done on countless other animals to try to develop immunity to dementia and Alzheimers. In the agricultural industries of the world, new types of corn, tomatoes, rice, and other types of crops are engineered on a daily basis, and new versions of these plants are made very commonly. The problem, however, is that a vast quantity of these plants are rejected from being planted. Some plants that are engineered either taste too bad, or they are less efficient than the plant at which they were modifying. As far as inventing a new species, you have to be more specific as to what you are asking. If science creates a new animal from another animal, it is likely of the same family and genus, like breeding a dog from another dog. Creating another type of mammal or reptile or bacteria that isn't part of a specific genus would be a breakthrough, as I am sure that all types of cloning and scientific pairing have been done to the same general Genus and Species... I am assuming, however, that it will be possible to engineer lifeforms at the molecular level by the next 50 to 100 years, as science and technology is getting more and more advanced. So, by the next few centuries, it would only seem logical to assume that new species would be created. However, the practice of creating new species, or even operating a laboratory/facility that deals with the concept, is illegal in a large number of countries, and has several guidelines in others.

I am only 13, so if any of this information is to be used anywhere else, I would advise not to cite me as a credible source. All this information is from my knowledge, and my knowledge is from school studies and personal readings. This is all my information, though. If any wording sounds similar to another source, keep in mind that one human brain functions similarly to another on several accounts and coincidences are often found.  I can assure you that if the documented information above is verified by plagiarism experts as my own wording, as I have taken the liberty to scan my own work. I hope I answered your question, and I am sorry for the long disclaimer ranting of this paragraph.


Peruvian insect identification The above is an insect I found while visiting Peru. I’m no biology expert, and I was just curious to know what species of insect this was. I found it on a rock while exploring the ruins near Pisac, if that helps.

Definitely not Megaloptera. Looks like a lampyrid (firefly) larval or female form. Note especially what look like single tarsal claws (on the end of the feet). This is diagnostic for Lampyridae (Coleoptera).


Which sequence characteristics influence the transcription efficiency of T7 polymerase? The T7 polymerase doesn't transcribe all sequences equally well, the transciption efficiency can vary widely for different sequences. One well known requirement of the T7 polymerase is that the sequence should begin with 2-3 guanines for efficient transcription.

Is there any literature that quantified the effects of the sequence on the transcription efficiency? I'm mostly interested in the effect of the first few nucleotides, as changing other parts of the sequence is usually not possible.

By far the most important part is the very beginning of the transcript, especially the positions +1 and +2. The conservered consensus sequence in class III T7 promoters is GGGAGA, any changes in the first two nucleotides severely reduce the transcription efficiency. Changes at positions +3 to +6 have much smaller effects.

Additionally, changes that put many AU base pairs in that region (e.g. GGUUU) seem to affect the trancription efficiency negatively.

Other sequences that are problematic anywhere, not only in the beginning are long stretches of uridines or adenines. Sequences with eight or more uridines or adenines can cause the polymerase to slip, which results in transcripts with more uridines or adenines than in the template.

These characteristics are detailed in the paper from Milligan and Uhlenbeck from 1989.

Milligan, J. F. & Uhlenbeck, O. C. Synthesis of small RNAs using T7 RNA polymerase. Meth. Enzymol. 180, 51–62 (1989).


Can oxygen diffuse out through the lungs? Let's say you accidentally walk into a room pressurized with pure nitrogen (or you're jettisoned into space). Within a couple of seconds, the partial pressure of oxygen within your lungs drops to 0. But there's still a (small?) reserve within your bloodstream.

Now, will the oxygenated blood travel to your lungs? If so, will the usual gas exchange reverse, with oxygen going from your blood to the oxygen-poor environment?

Yes.  Blood will continue to circulate (as long as you're alive and your heart is beating), so will eventually come in contact with your lungs.  Once there, the gasses (O2, CO2) will cross out into the lung and be exhaled.  All diffusion is driven down a concentration gradient.


Identify this plant from the Netherlands with big white flower The picture was taken today in the Netherlands. Can you identify this plant species?

Like @skymningen thought, this is a Clematis. However, the only wild Clematis in the Netherlands is Clematis vitalba, that has much smaller flowers (about 2 cm diameter) see "Heukels' Flora van Nederland" (the official Dutch flora) and here.

So you have photographed a plant that "escaped" from a garden. Most garden Clematis are hybrids from Chinese or Japanese origen. As there are about 300 species and new hybrids constantly being produced, the likelyhood of finding it's name is low. https://en.wikipedia.org/wiki/Clematis


What is the name of this beautiful insect? I spotted this magnificient looking insect last night in my house in Singapore. It was around 1.5 inches long and had a silverish golden back with long legs and antennae.

 ^ Click for full-size, higher-quality image

 ^ Click for full-size, higher-quality image

This is indeed a true bug (Hemipteran) in the infraorder Pentatomomorpha.
As Arthur Frost said in his comment, exact identification is difficult for those of us on the other side of the world.

However, a fortuitous series of internet rabbit holes may have led me to a very similar looking specimen.

Homoeocerus striicornis and Homoeocerus angulatus appear to be quite similar in appearance to your insect, and so I would not be surprised if your insect was at least in this genus (see here for more pictures) within the "leaf-footed bugs" family (Coreidae).

I'd say Homoeocerus angulatus is more likely only because the sightings maps on inaturalist show this species being found in Singapore.

I can't say that any incredibly reputable or peer-reviewed resources in English online provide definitive support for this identification, but this is at least a step in the right (a?) direction.


Transport of newly synthesized proteins to cellular organelles In the nucleus the DNA is transcribed and processed to mRNA which is translated into proteins in the cytoplasm. What happens between the time a protein is made and that when it reaches the cellular organelle in which it functions? How is it transported to its destination?

Mature RNA is translated into proteins by the ribosomes.  Ribosomes bound to the ER (endoplasmic reticulum) translate proteins that are bound for export from the cell.  Free ribosomes, which are found in the cytosol, are used for structures within the the cell (http://www.brighthub.com/science/medical/articles/110037.aspx)

Proteins made on the ER are sent to the Golgi apparatus, and are packaged there for transport out of the cell. (http://www.ncbi.nlm.nih.gov/books/NBK9838/)

As far as I know, the proteins made by free ribosomes remain in the cytosol and are incorperated into certain organelles or pathways upon contact with specific other proteins or signalling molecules.


Why isn't there T2 thyroid hormone? The follicles in the thyroid, intake iodine and bind them onto the tyrosine rings (attached to the thyroglobulin). This produces either MIT or DIT (tyrosine rings with 1 or 2 iodines attached respectively).

Then the DIT joins with either another DIT or a MIT to form T3 or T4. This makes sense.

But it seems to me, that there could be a MIT attaching to another MIT, forming T2. Why doesn't T2 get created?

In fact, there are two T2 hormones, depending on the position of iodine atoms on the thyronine backbone molecule [5].
One of them, 3,5-diiodothyronine (3,5-T2) is the most active of all thyroid hormones with a relative T4 potency of 8 to 15. Thereby, it is 2 to 5 times as potent as T3. Its plasma concentration is rather low, however, being 0.2 to 0.37 nmol/l [1–3]. It is weakly bound to plasma proteins and has a short half-life [7, 8]. 3,5-T2 seems to be a risk factor for atrial fibrillation [3], and it is able to suppress pituitary thyrotropin (TSH) secretion [4]. It is upregulated in critical illness (NTIS/TACITUS) [1, 3, 6].
The second isomer, 3’,5’-T2 is an inhibiting thyroid agent that is able to block the activity of deiodinases and receptors for thyroid hormones, similar to reverse-T3 (rT3) [5].

References

Pinna G, Meinhold H, Hiedra L, Thoma R, Hoell T, Gräf KJ, Stoltenburg-Didinger G, Eravci M, Prengel H, Brödel O, Finke R, Baumgartner A. Elevated 3,5-diiodothyronine concentrations in the sera of patients with nonthyroidal illnesses and brain tumors. J Clin Endocrinol Metab. 1997 May;82(5):1535-42. PMID 9141546. https://pubmed.ncbi.nlm.nih.gov/9141546/
Lehmphul I, Brabant G, Wallaschofski H, Ruchala M, Strasburger CJ, Köhrle J, Wu Z. Detection of 3,5-diiodothyronine in sera of patients with altered thyroid status using a new monoclonal antibody-based chemiluminescence immunoassay. Thyroid. 2014 Sep;24(9):1350-60. doi: 10.1089/thy.2013.0688. Epub 2014 Aug 1. PMID: 24967815. https://pubmed.ncbi.nlm.nih.gov/24967815/
Dietrich JW, Müller P, Schiedat F, Schlömicher M, Strauch J, Chatzitomaris A, Klein HH, Mügge A, Köhrle J, Rijntjes E, Lehmphul I. Nonthyroidal Illness Syndrome in Cardiac Illness Involves Elevated Concentrations of 3,5-Diiodothyronine and Correlates with Atrial Remodeling. Eur Thyroid J. 2015 Jun;4(2):129-37. doi: 10.1159/000381543. PMID 26279999. https://pubmed.ncbi.nlm.nih.gov/26279999/
Pietzner M, Lehmphul I, Friedrich N, Schurmann C, Ittermann T, Dörr M, Nauck M, Laqua R, Völker U, Brabant G, Völzke H, Köhrle J, Homuth G, Wallaschofski H. Translating pharmacological findings from hypothyroid rodents to euthyroid humans: is there a functional role of endogenous 3,5-T2? Thyroid. 2015 Feb;25(2):188-97. doi: 10.1089/thy.2014.0262. PMID 25343227. https://pubmed.ncbi.nlm.nih.gov/25343227/
Hoermann R, Midgley JE, Larisch R, Dietrich JW. Homeostatic Control of the Thyroid-Pituitary Axis: Perspectives for Diagnosis and Treatment. Front Endocrinol (Lausanne). 2015 Nov 20;6:177. doi: 10.3389/fendo.2015.00177. PMID: 26635726; PMCID: PMC4653296. https://pubmed.ncbi.nlm.nih.gov/26635726/
Langouche L, Lehmphul I, Perre SV, Köhrle J, Van den Berghe G. Circulating 3-T1AM and 3,5-T2 in Critically Ill Patients: A Cross-Sectional Observational Study. Thyroid. 2016 Dec;26(12):1674-1680. PMID 27676423. https://pubmed.ncbi.nlm.nih.gov/27676423/
Louzada RA, Carvalho DP. Similarities and Differences in the Peripheral Actions of Thyroid Hormones and Their Metabolites. Front Endocrinol (Lausanne). 2018 Jul 19;9:394. doi: 10.3389/fendo.2018.00394. PMID: 30072951. https://pubmed.ncbi.nlm.nih.gov/30072951/
Köhrle J, Lehmphul I, Pietzner M, Renko K, Rijntjes E, Richards K, Anselmo J, Danielsen M, Jonklaas J. 3,5-T2-A Janus-Faced Thyroid Hormone Metabolite Exerts Both Canonical T3-Mimetic Endocrine and Intracrine Hepatic Action. Front Endocrinol (Lausanne). 2020 Jan 8;10:787. doi: 10.3389/fendo.2019.00787. PMID: 31969860; PMCID: PMC6960127. https://pubmed.ncbi.nlm.nih.gov/31969860/


Preparing sample for SDS PAGE I have more than 10 cell lysate samples (70 µL each) whose concentration varies from 1.9 mg/mL to 4.8 mg/mL. I have 5X and 2X SDS sample buffers. I would like to prepare SDS PAGE samples in such a way that the final concentration of all the protein samples would be equal. I am struggling to deal with it.

What I know is while using 5X buffer, for 4 parts of sample we use 1 part of buffer to make it finally 1X. Similarly, for 2X buffer, we use equal amounts of buffer and sample to make 1X. Also, I would like to know will it be a problem if I make it more than 1X? Why we need 1X?

Usually you would want to keep the amount same, not the concentration. However, if you still want the concentration to be the same then you can add suitable amounts of PBS or your lysis buffer.

For e.g. if you have two samples with 1mg/ml and 4mg/ml concentrations and you want to load 20μg of total protein, then you can take 20μl of first sample and add 5μl of 5x loading buffer. For the second sample, you would take 5μl of the sample, 5μl of 5x loading buffer and 15μl PBS.

  Why 1x?

Because researchers before us found this composition to be optimal (or just simply stuck to it as a matter of practice).

  Would it be a problem if the final concentration of the loading buffer is more than 1x?

Apparently not, in my experience if it is up to 1.5x. Never checked higher concentrations.


Sexual selection in cats or other animals I was wondering if you could answer some of my questions regarding sexual selection in cats (or any other animals). I would like to apologize beforehand for my incorrect term use.

When it comes to mate choice, is mutual choice for both males and females the norm? If not, is it mostly a tomcat or a female cat who does the choosing?
Do female cats always have freedom to choose, or is it more like a rape or consensual sex?
How do cats choose their prospective partners in the wild, what are the mechanics of this process? Does a prospective partner come with the territory or are there any courtship rituals? I am interested in mate availability for female cats and sexual selection from a female cat perspective.

Thank you very much in advance.

P.S. Any other animals will do if they do not live in groups, prides or harems. I am interested in individual choices.

Wilson and Reeder (Mammal Species of the World) count 40 species of Felidae. Most of them are small cats (subfamily Felinae). Lions are in the subfamily Pantherinae, which contains only 6 species, one of them the jaguar, Panthera onca, which is solitary, like the tiger, Panthera tigris. By what I know of small cats, Puma concolor included, and the tiger and the jaguar, it seems that lion social behavior is not typical of felines. (Would add that as a comment, but can't comment with reputation < 50).

EDIT:

Looking for "Felidae sexual selection" or 'Felidae "sexual selection"' in google I have found some links. Look for "sexual selection" or "Felidae" in the text. Though I'm afraid most of them are not exactly what you're looking for, maybe they can open new windows of thought. Hope that helps!

http://www.journals.elsevierhealth.com/periodicals/aaeth/article/0304-3762%2883%2990116-5/

http://www.catsg.org/cheetah/05_library/5_3_publications/E/Eaton_-_The_Evolution_of_Sociality_in_the_Felidae.pdf

http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8312.2010.01520.x/pdf

http://www.jstor.org/discover/10.2307/3544917?uid=26584&uid=3737664&uid=5909624&uid=2&uid=26582&uid=3&uid=67&uid=62&sid=21103320511793

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

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0048352?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+plosone%2FPLoSONE+%28PLOS+ONE+Alerts%3A+New+Articles%29

http://books.google.com.br/books?id=FhvmHW972mAC&pg=PA752&lpg=PA752&dq=Felidae+%22sexual+selection%22&source=bl&ots=Ns8iRUQxXW&sig=r5ZEgp-nH9mll5cYgB5GzNaThZs&hl=en&sa=X&ei=FBPQUq63LPDLsQS0m4DAAw&ved=0CDYQ6AEwADgK#v=onepage&q=Felidae%20%22sexual%20selection%22&f=false

http://www.mapoflife.org/topics/topic_203_Baculum-%28penile-bone%29-in-mammals/

http://www.sciencedirect.com/science/article/pii/S0169534703003999


Gene Complementation Question Hi everyone! Here is a diagram of a genetics complementation problem. My main concern is regarding number 3d. I'm assuming that in this case, it would be complementary interaction and thus exhibiting a ratio of nine to seven. because if we cross F1, 3 will be mutant while one will exhibit wild-type phenotype. Is this right? Thanks in advance!

Yes 9:7 seems to be the right answer.

F1 progeny should be AaGg... and crossing it will give a ratio of 9:7 as is of any complementary genes


Beetle identification - Kakadu NP, NT, Australia I am trying to ID this beetle;

Size: not too big - approximately 2 cm (3/4 inch)
Where: Litchfield National Park, Northern Territory, Australia;
When: Southern hemisphere's spring, early September; the end of the dry season;
Time of day: night.

To my untrained eye, it looks like a cockschafer, but from the linked wiki page I understand they are a species confined to Europe. I tried a reverse Google image search and sifted through the site of Parks Australia and related pages, but to no avail.

After a hint from @fileunderwater I also think now that it is much more likely that this beetle belongs to the family of the Scarabaeidae which contains some 30.000 species worldwide. Scarabaeidae and Trogidae (what I thought was right before) are part of the same superfamily, the Scarabaeoidea.

The way the antennas are shaped as well as the body shape and the way the legs are ordered looks pretty much like this, even better than for the Trogidae. Have a look at this poster which shows a lot of different varieties (from here):

Some more information and real images can be found here and here.


Is the cranial nerve blood supply encapsulated by the blood brain barrier? I understand the origin of cranial nerves are within the blood brain barrier. I'm assuming as they extend distally there's a point at which their vasculature is not encapsulated by the blood brain barrier. Is this true? Any idea where the blood brain barrier stops?

Thank you.

I can't find a great answer to this either, but there is a known concept of a CNS-PNS transition zone, specifically as it pertains to myelination of cranial nerves. With the exception of CN 1 & 2 (which are effectively wholely CNS) the other cranial nerves are anatomically similar to spinal nerves, i.e. they're myelinated by Schwann cells and have an endoneurial blood supply. But they are also myelinated by oligodendrocytes for a short distance (varies by nerve) after taking of from their CNS nuclei before reaching that transition zone. According to this paper, that transition zone should mark the end of the astrocyte coverage which is necessary for BBB function. It's not a dead-ringer of an answer but this explanation makes as good physiologic sense as anything I've seen.

https://www.ncbi.nlm.nih.gov/pubmed/10697296


Why do we produce so many sperm? So apparently we produce roughly 300 million sperm daily. Is there a reason why this is necessary? Wouldn't a much smaller (but still large) number be sufficient? Like, one million?

The term you should look up is sperm competition, there is an introductory wikipedia article about it here, where you can get the basic picture and get some references to explore.

Simply said, males often compete with other males in the reproductive tract of the female, thus a higher number of sperm will lead to a higher chance of fertilizing the female in competition with other males - leading to an arms-race of the number of sperms a male eject into the female.

There is a lot more to it, of course, but I believe this well explains the most fundamental driver of why males generally produce and eject so many sperms.


What does "each pathway define an independent genotype" mean? In a section of this paper.

  However, if the question of independency is posed in the
  form: “Does each pathway shown define an independent
  genotype?,” then each of these three pathways is indeed
  independent. This is the way that MPS defines the independence
  of pathways.

What does “Does each pathway shown define an independent
genotype?,” mean?

This is somewhat outside my field, but basically it seems they're defining the independence of the three hypothetical metabolic pathways in two different ways:

Mathematically the pathways are not independent since P₃ is a combination of P₁ and P₂.
Biologically the pathways are independent since each requires a different combination of enzymes and therefore genes (the genotype). This is the method used in MPS.

Does that answer your question?


How does one measure the length of telomeres? My questions are:

What techniques are available for doing so?
Are they destructive ?
What is their accuracy ?

Again, not an expert, but I found this article seems to say it pretty well:

Telomere's are most commonly measured by qPCR of the repetitive regions with degenerate oligomer sequences such as "TTAGGG and CCCTAA repeats"  Although articles like this one appear to advance measurements in vertebrates, this reference from 2011 implies two techniques continue to be most common:

1) qPCR with the appropriate oligos and then running them on an agarose gel

2) Southern blot of a restriction digest that leaves the telomeres intact

Clearly sequencing techniques don't do well with repetitive sequences such as this, so in general this still seems like the most common method.

This would indeed be quite destructive, at least for the cells used, though a biopsy would be enough, though apparently micrograms of DNA are required.  Kind of a large amount.

The accuracy would then be limited to that of the gel or blot.  That would generally be a percentage of total length, I think 2% might be obtainable, but I'm not sure about that part.


Are there known functions of AST, ALT, and amylase in the blood? A number of enzymes can be measured in the blood or plasma that aid in the diagnosis of certain diseases. For example, patients with particular liver diseases may have elevated aspartate aminotransferase (AST) and/or alanine aminotransferase (ALT) levels in the blood. These enzymes are normally involved in biochemical reactions of metabolism that interconvert amino acids with other metabolic intermediates - that is, biochemical reactions that are common within the liver cell. Also, patients with pancreatitis frequently have elevated amylase and lipase levels, which are digestive enzymes normally secreted into the gastrointestinal tract. During pancreatitis these enzymes are released into the blood, rising and falling with the resolution of pancreatic damage/inflammation.

Pathologically, the tissues that are damaged in these diseases (liver and pancreas, respectively) are the source of the elevated enzymes. In healthy individuals, however, these same enzymes are still found in low concentrations in the circulating blood. What is the source of these enzymes that are found in low circulating concentrations? Is it still those same tissues (e.g. AST/ALT from the liver)? Is this secondary to "normal turnover" of cells within those tissues? Or, alternatively, are these enzymes secreted into the blood to serve a particular function?

For example... There is a freely available manuscript by Arnold and Rutter published in the Journal of Biological Chemistry (1963) that discusses experimental evidence for active amylase secretion from the liver during an isolated liver perfusion experiment. Amylase continues to be secreted, even in the absence of other enzymes that would otherwise indicate liver damage (suggesting that the amylase is intentionally being secreted for some unknown purpose). This is an paper from almost 60 years ago - do we know what some of these enzymes like AST/ALT and amylase do in the plasma? Or are those functions still unknown?

These enzymes, while useful markers of disease, are not only produced during the disease state, and are not only produced in one organ. It is therefore not surprising that there are always low levels released into the biochemical milieu that is the blood. If there are not even low levels of the enzymes then that might indicate that the organ is not doing it's job properly.

I'll approach this from a veterinary viewpoint but I imagine it is much the same in humans. My preferred source for information about veterinary clinical pathology is Cornell's EClinpath site.

The major tissue sources of AST are liver, skeletal muscle, and cardiac muscle. A small amount is produced by erythrocytes. In lesser concentrations it is also found in renal epithelial cells and brain tissue. It therefore should be no surprise that low levels are found in blood. It is not difficult to picture a small amount of leakage from erythrocytes in the normal state, even without pathologic haemolysis, given the regular turnover of cells and permeability of erythrocytes – although I suspect this is a minor source. Just due to the fact that the liver's normal function is to deal with many cytotoxic compounds, even in the completely healthy patient there always is going to be some low level of hepatocellular damage. As a result, a very low serum level of AST might be indicative of a poorly functioning liver (e.g. with a chronic hepatitis).

Among veterinary species there is considerable variation in the clinical usefulness of ALT. For example, it is a very useful indicator of liver disease in dogs and cats, much less so in horses. Much like AST, ALT is also produced in liver, muscle, kidney, and erythrocytes.

Amylase is known to be produced by cells in the pancreas, salivary gland, duodenum, ileum, ovary, and testes. Of course, the pancreas produces the most of this enzyme, which is why it is somewhat clinically useful (though I can't say I like it much at least for veterinary species).

The bottom line is that these enzymes play an important role in biochemical reactions of many different tissues. While the enzymes may be produced in predominance in one tissue, they have the same function (at a biochemical level) in all these tissues (i.e. they convert the same reactions). I view it more as a difference of the tissue need for these enzymes rather than a difference in function between tissues.


How can electric fields inhibit tumor growth? In MIT's Technology review it is explained that electric fields can cause dividing cancer cells to explode, while these fields have no significant impact on non-dividing tissues. The original research was done by Palti et al.

What is the mechanism behind this? It does not seem to be related to thermal effects.

Edit: The treatment in question seems controversial. A clinical trial showed improvement but it is not rock-solid data.

In a PNAS paper by Palti's group (2007) they explain the hypothesis behind the technique:

They reason alternating currents of 100 kHz to 1 MHz specifically affects dividing cells and thereby targets cancer cells. Note that this is the same basic idea as chemotherapy and radiotherapy, which also target dividing cells mostly. The mechanism of action of alternating electric fields on dividing cells is though to be the result of a specific effect on the  bridge separating the daughter (cancer) cells during cell division (Fig. 1). They think it interferes with spindle tubulin orientation and induces electrophoretic effects (Kirson et al., 2007), resulting in a pile-up of cytoplasmatic organelles at the cleavage furrow. This is thought to interfere with cytokinesis, and to lead to cell destruction** (Kirson et al., 2004).

Note it is the frequency that differentiates between the various effects of current stimuli. At very low frequencies (1 KHz) electric fields stimulate excitable tissues through membrane depolarization. At higher frequencies this excitatory effect is lost. At very high frequencies (>1 MHz) tissue heating results (e.g., microwave ovens).  Hence, alternating electric fields of intermediate frequencies (10 kHz to 1 MHz) were considered not to have any meaningful thermal effects (Kirson et al., 2004).

Fig. 1. Palti's electric field hypothesis. Source: Kirson et al. (2007)

References
- Kirson et al., Cancer Res (2004); 64: 3288-95
- Kirson et al., PNAS (2007); 104(24): 10152–57


How is epinephrine and norepinephrine different? Is there any difference between epinephrine and norepinephrine?

https://www.quora.com/What-is-the-difference-between-epinephrine-and-norepinephrine

This site says that norepinephrine is also a neurotransmitter.

Is there any major difference between them?

But little amount of epinephrine also serve as a neurotransmitter.

Iam mentioning here some of the differences I found out myself when I had the same question.

If you need further reading you can visit the site  as mentioned by @Spartacus9
https://en.wikipedia.org/wiki/Epinephrine
https://en.wikipedia.org/wiki/Norepinephrine

1)Norepinephrine is mostly made inside nerve axons and released when an action potential travels down the nerve.

Epinephrine is made from norepinephrine inside the adrenal medulla.

2)Norepinephrine acts mostly on alpha receptors.

Epinephrine is relatively non specific,stimulating both alpha,beta1,beta2,beta3 receptors more or less equally.

3)In medicine, norepinephrine is used to increase and maintain blood pressure related to cardiac arrest,spinal anaesthesia,septicaemia,etc.

Epinephrine is used in medicine to treat low blood pressure associated with septic shock and also for the emergency treatment of allergic reactions.


What is the role of the pyrrolidine/piperidine moieties in fagopyrins? Fagopyrins are phototoxic compounds that cause fagopyrism. They are chemical compounds related to hypericin and pseudohypericin. Some variations lack one or both methyl groups, which I think is to streamline the molecule so it better fits in membranes and so increase damage. The main difference from (pseudo)hypericin though is the presence of pyrrolidine or piperidine (or both) moieties, which may come from L-proline and L-piperidine-1-carboxylate (in turn from L-lysine) respectively. So, what is the function of those moieties in the fagopyrin molecules? Does it render fagopyrins more toxic than (pseudo)hypericin?

Radical generator

Looking at the molecules they are highly conjugated —must be dark red or similar!
And the disease is photosensitivity. Aromatics + UV? That is a standard UV radical reaction. It may be enough as a catalyst, but you'll get more will a cyclic amine, such as pyrrolidine or piperidine. If you want to go technical confer: Hofmann–Löffler reaction.

The radical will be passed on to other molecules, such as oxygen (generating peroxide), which will damage DNA and will raise an alarm biologically ultimately attracting neutrophils, which are expecting some attack (not poisoning), thus causing local inflammation, which manifests as skin irritation.

Demethylation

With the caveat that secondary metabolism is highly promiscuous and that some modifications are more accidental that anything else, let's look at the methylation and membrane permeability.

Promiscuity and secondary metabolism evolvability

This figure I found has the methylation patterns. A first glance I have assumed it was the usual C-methyltransferase action adding methyl groups, but instead it is a removal twice in the case of fagopyrin B and once in C and D. Specifically, fagopyrin is clearly two condensed anthraquinones molecules (emodin?) —which is a rather interesting non-standard change, I have not looked but so hope that someone has found the enzyme responsible! As you point out an anthraquinone is made by polyketide synthesis: the last acetyl-CoA results in a methyl group on the aromatic structure, which is occassionally oxidised to a carboxyl group (e.g. rhein) and in this case decarboxylated —I do not think a C-methyltransferase can remove groups even with pushed stoichiometries nor do I believe I have heard of one. But anyway. The anthraquinone condensing enzyme may not be able to tell apart the standard and the demethylated metabolites, which is otherwise meant for another pathway, i.e. it could just be promiscuous.

Membrane

Let's calculate the effect on solubility (python3 w/ RDKit).

Wikipedia has the SMILES string for the main fagopyrin and it's easy to spot the methyl groups.

from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem.Draw import SimilarityMaps
# let's make the molecules
normal = Chem.MolFromSmiles('O=C1C2=C(C3=C(O)C(C4CCCCN4)=C2O)C(C5=C6C(C)=CC(O)=C15)=C7C(C3=C(O)C(C8NCCCC8)=C9O)=C9C(C%10=C7C6=C(C)C=C%10O)=O')
demeth = Chem.MolFromSmiles('O=C1C2=C(C3=C(O)C(C4CCCCN4)=C2O)C(C5=C6C=CC(O)=C15)=C7C(C3=C(O)C(C8NCCCC8)=C9O)=C9C(C%10=C7C6=CC=C%10O)=O')
# no need to orient them as the indices are the same. Whoohoo
img=Chem.Draw.MolsToGridImage([normal, demeth],
                              molsPerRow=2,
                              subImgSize=(200,200),
                              legends=['w/ methyls', 'w/o methyls'],
                              useSVG=False).save('/Users/matteoferla/Desktop/mols.png')

Now let's calculate logP (Partition coefficient).
    print('w/ methyls', Descriptors.MolLogP(normal))
    print('w/o methyls', Descriptors.MolLogP(demeth))

w/ methyls 6.71
w/o methyls 6.0

They are really soluble in octanol and insoluble in water. The unmethylated version is less hydrophobic.

Let's look at what is causing the difference by looking at the Crippen contributions to logP. Using the BluePurple colormap (suggestions welcome for best colormap for this descriptor), so that purple is hydrophobic while light blue is hydrophilic. Note that this is not partial charge (Gasteiger).

for mol, name in ((normal, 'meth'),(demeth, 'demeth')):
    AllChem.Compute2DCoords(mol)
    contribs = Chem.rdMolDescriptors._CalcCrippenContribs(mol)
    fig = SimilarityMaps.GetSimilarityMapFromWeights(mol, [x for x,y in contribs], colorMap='BuPu', contourLines=10)
    fig.savefig('/Users/matteoferla/Desktop/'+name+'_crippen.png', bbox_inches='tight')

The difference is a result of the methyl groups, being slightly more electron withdrawing than hydrogens making the carbon between it and the hydroxyl/ketone more hydrophobic. But overall does not change the polar sides, so is in effect unlikely to have an effect on its high membrane permeability.


How do warm-blooded animals keep their temperatures constant? Warm blooded animals like us keep their temperature constant irrespective of their surroundings. But how do they do that? Energy should be supplied from the inside. I assume that reactions like making ATP from glucose are exothermic. That means in winter our body reacts more. Water is absorbed by those reaction.We should need more water in winter. Which is contradictory with our real life experience.

On the other hand what prevents cold blooded animals from making heat? Don't they need ATP? Do they use different types of reactions to make energy? Do they have different evolutionary path? They don't seems very different from us.

Since there seems to be several distinct sub-topics in your question, I will answer them one-by-one:

1). There are a variety of mechanisms that allow endothermic animals to maintain thermal homeostasis in a cold environment. The main ones are:

a). The shivering response: When the core body temperature of a endotherm drops below a critical value (36.8C in humans), it causes the posterior hypothalamus to stimulate certain skeletal muscle groups (especially around vital organs) to start to "shiver" rapidly, generating heat.

b). Compared to ectotherms, endotherms have more mitochondria per cell, thus allowing them to have a higher metabolism. Since metabolism always generates heat, an [general] increase in cellular metabolism will cause an increase in body heat.

c). Many endotherms have layers of insulating matter, such as fur, blubber, feathers…etc, allowing them to preserve body heat. In addition, endotherms can also route blood away from  capillaries via vasoconstriction of arterioles, reducing the area in which heat can be lost.

d). As mentioned by Memming, brown adipose tissue also plays a role in temperature regulation. Thermoregulation-based metabolism in brown fat causes the P+ in the electron transport chain to go through thermogenin instead of ATP synthase. This process generates heat, but no ATP.

e). Some endotherms, such as penguins and arctic wolves have countercurrent exchange in their capillaries. This is when warm arterial blood "passes" some of its heat to cooler veinous blood. This feature allows some of the heat normally "wasted" into the air to be recycled back into the body.

Note: Though it is true that endotherms are able to keep their body temperature constant irrespective of their surroundings (ignoring extremes), they do this at a cost of requiring significant amounts sustenance. Most endotherms require much more sustenance than ectotherms.

2). Your second sub-question is very interesting. Though it is true that generating heat will require substantial amounts of carbohydrates/fats/...etc, it does not necessarily mean that the net consumption of sustenance in cold environments is greater than that in normal environments. In most cases, endotherms in cold environments will have exhibit significantly less activity than when in an optimal environment. The decrease in activity when in a cold environment will likely balance out the increase in thermo-regulation based metabolism. This likely explains why people tend to drink equal or slightly less amounts of water when in cold environments. One more thing: some reactions heat-generating reactions (like the alternate ETC pathway) do not require water. Glycolysis and Krebs actually generates water (not to say that there is a net gain in the body :))

3). In truth, nothing "prevents" ectotherms from generate heat. They simply do not have the cellular "machinery". Ectotherms metabolize in ways very similar to other organisms, using molecules like ATP, glucose, fat…etc. Unlike endotherms however, they spend very little of their energy on temperature regulation. As a consequence, their overall metabolic rates are dependent on the external temperature. The point is this: A substantial portion of endotherm sustenance is used to generate heat. Only a small (if any) portion of ectotherm sustenance is used to regulate heat. As a result, endotherms require much more nourishment than ectotherms.

4). I am not entirely certain what you mean by "evolutionary path", but I will just say this: In many ways, endotherms and ectotherms are organisms that have found different ways to the same problem; how to regulate body heat for maximal survival and reproduction. Basically,

ectotherm- more dependent on environmental temperature, requires less sustenance

endotherm- less dependent on environmental temperature, requires more sustenance

5). You are quite correct. The cellular and genetic components are very similar. Some morphological aspects seem to be shared as well.

  Sources:

  Cambell & Reece (2010) Biology (9th ed)

  Swan, K. G.; R. E. Henshaw (March 1973), "Lumbar sympathectomy and
  cold acclimatization by the arctic wolf", Analysis of Surgery 177 (3):
  286–292,

  Guyton & Hall (2006) Textbook of Medical Physiology. (11th ed)

  Romanovsky AA. (2007). Thermoregulation: some concepts have changed.
  Functional architecture of the thermoregulatory system. Am J Physiol
  Regul Integr Comp Physiol. 292(1):R37-46.


Energetics and Products of Pepsin/HCl Protein Digestion What are the energetics of protein digestion during which the enzyme pepsin is "activated" (whatever that means) by HCl?  I've looked and been unable to find anything like a chemical equation that includes an energy term.

Of course, pepsin, being an enzyme, is not used up in that sought-for equation.  Is HCl used up?  If so, what are the products?  How and in what form is the chlorine removed, assuming the HCl is consumed in the equation?

This is well-explained on the Wikipedia page for pepsin. You are misinterpreting the use of the word activated. The protein is secreted by chief cells in the gastric glands in the form of pepsinogen, an inactive pro- form which has an extra ~40 amino acids at its N-terminus (the propeptide). The propeptide binds at the catalytic site of the enzyme and keeps it inactive. At low pH (this is where the HCl comes in - HCl secreted by parietal cells of the gastric glands acidifies the stomach) the protein is able to cleave off its own propeptide, making it fully active.


How does the immune system distinguish between a TH1 and a TH2 response? Hello and thanks for taking the time to read my post.

I know that naive T-Cells (T0) can be induced to become mature T-Helper cells (TH1 or TH2)
by induction with either IL2 or IL4.

IL2+  TH0 -> TH1   Humoral (antibody-mediated)
IL4+  TH0 -> TH2   Cell Mediated response

But what I would like to know is the causal chain that creates the IL2 and IL4 cytokines.

The reason I ask is because one clinician has reported that Azythromycin(an anti biotic) is useful in treating COVID-19(a virus) disease and was wondering if the immune system might become confused about whether should develop a TH1 or TH2 response.

If you can provide me with any help I would greatly appreciate it

Thanks in Advance
Michael Mckeon

From what I have read, the Stage 3 differentiation depends on the surrounding cytokine environment. IL-2 does not specifically promote T-Cell differentiation, it is a general growth factor which promotes proliferation, and is secreted by both profiles.

Differentiation of T-Cell into Th1 is controlled by Interferon Gamma, the production of which is stimulated by IL-12, which is secreted by many APCs (upon stimulation by IFN Gamma produced by cells, in a self-feeding loop). IFN Gamma also suppresses IL-4 production.

Th2 cells are promoted by IL-4. It is not exactly known which cell initially produces IL-4, but it could be basophils. IL-4 then acts in a self-promoting loop, which encourages T-Cells to produce IL-4 as well as other effector cytokines, and also stimulates IL-10 production, which suppresses production of IFN Gamma and IL-12.

Thus, each pathway is self-promoting and suppresses the other pathway, ensuring that the immune response is set in stone.


Why don't warts caused by HPV spread to the whole body? My son had a plantar wart on his foot, which (as I understand it) is caused by a virus which only infects skin cells. Once in the skin cell the virus replicates, but when attacked by the immune system prompts the growth of a hard, thick layer of skin (callus). Warts are caused by a HPV.

Given the wart has infected a skin cell, and skin cells are next to each other in a great big sheet covering the entire human body, why is it that we don't become completely covered in wart?  I assume that it's not the immune system keeping the wart at bay, because the original wart isn't defeated and we can get other spot infections elsewhere.

Plantar warts grow deep into the skin and slowly [1]. It is a common thing for warts to multiply [1], but because of the slow growth speed, their symptoms [2] and the self clear-up [1] they can't end up by covering the entire skin surface of a previously healthy person.

There are cases of generalized warts in patients with immune deficiency like hypogammaglobulinaemia, impairment of cell mediated immunity [3]. The immune system plays an important role in limiting warts. There is also a case of generalized facial warts in a patient with no other known medical condition [4].

References:

American College of Foot and Ankle Surgeons, Plantar Wart (Verruca Plantaris)
MAYO Clinic, Diseases and Conditions - Plantar warts.
Reid TM, Fraser NG, Kernohan IR. Generalized warts and immune deficiency. Br. J. Dermatol. 1976 Nov;95(5):559-64. PubMed PMID: 1086679.
Semon H. Papillomatosis: Generalized Facial Warts. Proc. R. Soc. Med. 1935 Dec;29(2):90. PubMed PMID: 19990539.


Premise of life cycle synchronization between predator and prey While reading about the predator satiation hypothesis of the periodical cicadas' 13/17 year life cycles, I started wondering about its premise. By the way, I understand the math behind the prime number life cycle. 13 and 17, being prime numbers are only divisible by themselves and 1, and thus have as few divisors as possible. But my question is about the premise of why a predator would even want to synchronize its life cycle with a divisor of the prey's life cycle in the first place.

If the predator has a set life cycle, but its individuals are evenly distributed in regards to their development within that life cycle at any given time (for example there could be roughly even amounts of mature and immature predators at any given time), then what difference does the life cycle make? Here I am assuming that eating cicadas is most beneficial to a specific developmental stage of the predators, which is the only reason I can think of why there would be an advantage to this synchronization. By the way, is this even a correct assumption in regards to this hypothesis?

To be clear, my main question is why life cycle synchronizations between predator and prey matter when/if predators aren't all undergoing the same stages of their life cycles simultaneously.

edit: To be even more clear, I am asking what the benefits are to the predator to synchronize its life cycle with the prey (the cicadas, in my example).

My reference: Wikipedia says the following: *It was hypothesized that the emergence period of large prime numbers (13 and 17 years) was a predator avoidance strategy adopted to eliminate the possibility of potential predators receiving periodic population boosts by synchronizing their own generations to divisors of the cicada emergence period.
Goles, E.; Schulz, O.; Markus, M. (2001). "Prime number selection of cycles in a predator-prey model". Complexity 6 (4): 33–38. doi:10.1002/cplx.1040.

I have interpreted "synchronizing their own generations to divisors..." to mean synchronizing the length of the life cycle. I am happy to hear of another interpretation.

New Answer, based on first comment by user2686410 and subsequent edits to the question.

  I have interpreted "synchronizing their own generations to divisors..." to mean synchronizing the length of the life cycle. I am happy to hear of another interpretation.

First, the overall goal of Goles et al. (2001) does not seem to test hypotheses related to the evolution of life cycles in the cicadas per se. It seems their overall goal instead may have been to explore the generation of prime numbers from numerical theory, using biologically-based models. For example, from the abstract they state,

  The model marks an encounter of two seemingly unrelated disciplines: biology and number theory. A restriction to the latter, provides an evolutionary generator of arbitrarily large prime numbers.

and at the end of the discussion they write,

  Although there are traditional methods for prime number detection (see e.g., Ref. 23) that are faster than the methods presented here, it is remarkable that the generation of prime numbers can be performed using a biological model.

To more directly address your question and if I understand their models, Goles et al. (2001) do seem to allow the the life cycles of both predators and prey to co-evolve yet this is not always clear.

  We compare now a prey mutating to a cycle Y' with the resident prey (cycle length Y ) at constant X. Analogously, we compare mutant cycles X' with resident cycles X at constant Y (Goles et al. 2001, pg. 34; emphasis added).

Here, they seem to be saying that the life cycle of one (predator or prey) can change while other other remains constant (prey or predator). The life cycles don't coevolve.  Subsequent formulas and statements imply an interactive effect between the predator and prey life cycles. (Honestly, their writing is somewhat opague to me and they do not define all of their mathematical terms, making it difficult to follow the logic of their models.)

Regardless, the results of their initial models, shown in the figure below, shows the prey converging on a 17 year life cycle while the predators converge on a 4 year cycle. Somewhat more complex models tended to converge on 13 and 17 year cycles, although other primes like 11, 19 and 23, had similar probabilities of evolving.

Goles et al. (2001) admit at the outset of their paper that there is no evidence for predators with periodical cycles that align with the life cycles of cicadas. This would be consistent with general ecological observations. Most predators consume multiple prey items. Highly specialized predators would be more vulnerable to extinction if their prey source went extinct.

Another numerical model, developed by Tanaka et al. (2009) explicitly to explore life cycle evolution of cicadas, does not include predator life cycles at all. Their results still converge on 13 and 17 year life cycles although they restricted the possible range of life cycles to between 10 and 20 years. Thus, it does not appear to be necessary for predators to evolve a life cycle that coincides with prey life cycles for the predator satiation hypothesis to work. Of course, this is consistent with the real world observations that cicadas do not appear to have predators with concommitant life cycles.

Original answer, lightly edited

In the case of the cicadas, they are the prey, not the predators. They are not synchronizing their life cycles with the predators (if I am interpreting your entire question correctly). The argument is that cicadas have evolved synchronized life cycles to maximize survivorship.  By having a large number of individuals emerge within a very short period of time, the very high density means most individuals will live long enough to reproduce because the predators (birds, small rodents, etc.) will be satiated (see Williams and Simon 1995 for a review and pointers to early literature). Some predators of cicadas will be always present so the cicadas are not synchronizing to any specific predator.

Goles et al. (2001) used numerical models to argue that such life cycles will tend to converge on prime numbers. (As discussed in the update above)

Tanaka et al. (2009) recently argued, again using numerical models, that the prime number-based life cycles of cicadas evolved as a result of the Allee effect. The Allee effect basically states that there is a positive association between the fitness of individuals in the population and the population size or density. Below a certain size, a population is unable to sustain itself and is vulnerable to extinction. Tanaka et al. argue that the Allee effect results in prime-based life cycles under varying environmental parameters. They further argue that maintenance of alternate life cycles minimize hybridization between groups with different life cycle timings.

What seems to really remain to understand the evolution of cicada life cycles is to unravel the genetic mechanisms involved with timing.

Literature Cited

Goles, E. et al. 2001. Prime number selection of cycles in a predator-prey model. Complexity 6: 33-38.

Tanaka, Y. et al. 2009. Allee effect in the selection for prime-number cycles in periodical cicadas. Proceedings of the National Academy of Sciences USA 106: 8975-8979.

Williams, K.S. and C. Simon. 1995. The ecology, behavior, and evolution of periodical cicadas. Annual Reviews of Entomology 40: 269-295.


Hill's function for translational regulation Transcriptional regulation is generally modeled as a Hill's function (similar to Michaelis-Menten Kinetics):

$$\frac{dm_X}{dt}=\alpha _{m_X}.\frac{R}{K+R} -\beta _{m_X}.m_X$$

Where $m_X$ is the mRNA for some gene-$X$, $R$ is a Regulator $\alpha$ and $\beta$ are formation and degradation rate constants respectively. This equation denotes a saturation kinetics; increasing activator wont cause indefinite increase in transcription. Sounds logical because all promoter sites will be occupied at some point.

In case of a repression the equation looks like:

$$\frac{dm_X}{dt}=\alpha _{m_X}.\frac{K}{K+R} -\beta _{m_X}.m_X$$

I want to model repression of translation using a similar equation. However, the issue is that even though a single mRNA can be saturated by a regulator, increasing mRNA will require more regulators. So effectively the regulator available for a single mRNA molecule will be total regulator ÷ total mRNA.

My question is that whether in such a case the following equation is logical:

$$\frac{dX}{dt}=\alpha _{X}.m_X.\frac{K}{K+R/m_X} -\beta _{X}.X$$

Where $X$ is the protein.

Which means we are taking into consideration the effective concentration of a regulator per mRNA. In other words the Hill's constant $K'$ should scale with mRNA concentration. ($K'=K\times m_X$)

Assumptions:

Well mixed system
System at thermodynamic limit
Amino-acid pool infinite
Ribosomes infinite

Your logic looks correct to me. Essentially, what you are doing is uniformly distributing the regulator among the available mRNA.

Note that even when using Hill functions to model transcription, the ratio of transcription factor (TF) concentration to the number of TF binding sites must be large - otherwise, you would have to consider binding ratios even at the level of transcription modeling, similarly to what you are doing now for translation. E.g. consider a hypothetical situation where 10 TF molecules compete for binding to 5 different promoter regions, each having 10 binding site repeats - you need to somehow distribute the available 10 TF molecules among 50 target binding sites. Clearly, this is not something accounted for by the standard Hill equation, which would in such case wrongly assume that 10 TF molecules are regulating each construct.

In your specific case, introducing the ratio of the regulator per each mRNA may not even be necessary if this ratio is large, effectively leading to saturation levels anyway. Note that the maximum level that $m_x$ can reach (at steady state) is equal to $max(m_X) = \frac{\alpha_{mX}}{\beta_{mX}}$. If you can ensure this value to be much smaller than your translational regulator concentration, you will get similar results even if you use simply $\frac{K}{K+R}$ for translation modeling.

If the latter assumption cannot be made, then your reasoning makes sense. For each individual mRNA molecule:

$$\text{X produced per mRNA} = \alpha_{X} .\frac{K}{K+R'}$$

where $R'$ is the amount of mRNA bound to this molecule. If $R$ is the total available regulator concentration and uniform binding affinity is assumed, this means that $R'=\frac{R}{m_X}$. Summing this over a total of $m_X$ mRNA and considering degradation yields exactly your final ODE.

Note that another important assumption you are making is that regulator binding/unbinding to/from mRNA is fast compared to translation, and that no cooperative interactions are present.

If you want to verify things further, you could establish system reactions, then derive Hill-free ODE equations according to the law of mass action. You could then compare this model to the one you propose. Furthermore, performing a stochastic simulation might make sense. If you want to go down this road but don't want to implement Gillespie's algorithm on your own, you can use e.g. SGNSim or COPASI.


Chromosome and chromatid numbers during cell cycle phases A diploid cell in G1 has 6 chromosomes. How many chromosomes and how many chromatids are present in each of the following stages?

Here is what I am guessing

G1: 6 chromosomes ; 6 chromatids
G2: 6 chromosomes ; 12 chromatids
Prophase: 6 chromosomes; 12 chromatids
Metaphase: 6 chromosomes; 12 chromatids
Anaphase: 12 chromosomes; 12 chromatids
Telophase: 12 chromosomes; 12 chromatids

The chromosomes copy at S phase. So S/G2 checkpoint up to early anaphase has 2n. You are on the right track to understanding the cell cycle, important to note the differences between homologous chromosomes (homologous pair) and sister chromatids, while understanding  ploidy.

During S (synthesis) phase which occurs between G1 and G2 , all the somatic DNA replicates. So every chromosome gets copied and thus  has a sister chromatid.

Animals that undergo sexual reproduction have 2 sets of chromosomes, one from mom the other from dad. The chromosomes of each pair represents homologous chromosomes.

Your answer is almost correct. I believe it could be adjusted to:

G1: 6 chromosomes
G2: 6 chromosomes /12 chromatids Prophase: 12 chromatids
Metaphase:  12 chromatids
Anaphase: 12 separating chromatids
Telophase: 12 chromosomes, 6 one each pole of the cell

These very simple figures explain the principles I mentioned earlier


What is self-immunoreactivity? I read something like "some tested variants show self-immunoreactivity". So, what exacly is self-immunoreactivity? Is it something like antibodies induced by a specific variant showing immunoreactivity to this specific variant?

The basic concept of the immune system is that it has to discriminate between self and foreign and that is only allowed to launch an immune reaction against something foreign. This is called immune tolerance which basically makes sure that all immune cells which are directed against the own organism are destroyed.

If these antibodies survive, they can attack the own body (and are hence called self immunoreactive) and cause damage. Self-immunoreativity is a reaction of the body against itself. Problems with the immune tolerance are called autoimmune diseases, examples would be  systemic lupus erythematosus, rheumatoid arthritis or type 1 diabetes.


Why increasing the vector concentration does not increase the effeciency of bacterial transformation? I was reading some old description of the protocols used for the transformation of bacterial cells.

In the description I read that the transformation works best with low amount of DNA, and if we increase the amount of DNA used the amount of transformant cells does not increase proportionally.

I just wonder why, since in my eyes the process of entering the cell is mainly related to the diffusion principles, and therefore concentration dependent.

According to the Hanahan transformation protocol (one of the highest competencies published), a transformation of 200µl will contain $1×10^8 - 1.7×10^8$ cells.

Assuming that the pBR322 plasmid is used, 1ng of plasmid will convert to 0.36fmol of plasmid, or $6×10^8$ plasmid copies.

As we can clearly see, even at very low quantities of DNA used, there are multiple plasmids per cell. Since transformation is thought to be mediated by DNA channels, massively increasing the quantities of DNA would not equally increase transformation efficiency once all of these channels are saturated.

The example from NEB Turbo DH5α cells seems to show this quite well, that once DNA quantities exceed 1ng, the transformation efficiency drops precipitously.

This being said, if the amount of plasmids available is very large, there is no reason to avoid adding more than 1ng of DNA, as they would not reduce the total number of transformation colonies, but only the efficiency.


Why are there not two trees of life? Life on earth started an estimated 3.8 billion years ago, very soon (in geological time) after the earth’s surface cooled to become solid and the first oceans formed. Nowadays, we believe that all living things can trace their ancestors back through a multi-branched tree of life, to this first living thing.

How do we square this rapid appearance of life, with the fact that it only seems to have developed once? In other words, we didn’t have life starting up in 10 different places on earth, giving rise to 10 different trees of life, why did we see only one?

In a variation on Richard Dawkins’ Selfish Gene, is it possible to think about a Selfish Tree?

Once the first tree of life arrived, it set about changing the atmosphere and environment generally, multiplying the number and range of species to fill every available niche (eg cold, hot, land, river, ocean, acid, alkali, large, small) in order to leave no space or circumstance for a second tree of life to spring into being.

The emergence of life out of matter is a very rare event.
The chance of having such event occurring more than once in a small time-frame is very little.

If the time-frame is large enough, then "New Life" could emerge again. However, in that case, the new emerging living organisms would be extremely disadvantaged by the presence of the "Old Life", already evolved to efficiently compete for energy sources etc.

Any new, barely functional, primordial life form cannot outperform the already existing ones, thus it would undergo extinction pretty soon. And that is why we ended up with a single tree of life on this planet.

Some links for further reading:

http://www.science20.com/stars_planets_life/calculating_odds_life_could_begin_chance

http://www.science20.com/news_releases/the_mathematical_probability_of_life_on_other_earth_like_planets

https://www.sciencedaily.com/releases/2018/01/180108090109.htm

https://www.scientificamerican.com/article/universal-common-ancestor/

https://www.nature.com/articles/nature09014

https://link.springer.com/article/10.1007%2Fs00239-010-9407-2

https://febs.onlinelibrary.wiley.com/doi/abs/10.1016/0014-5793%2896%2900631-X

https://www.sciencedirect.com/science/article/pii/S0022519318300419?via%3Dihub


Is there a rule for the annotation of the basepair or gene locus origin in bacterial genomes? Since all bacteria have one circular chromosome, there is no designated origin to start the systematic gene locus numbering. Therefore, what is the rule to start the numbering at a particular point (i.e. why is in the E.coli K12 strain the thrL gene given the ordered locus number b0001? If the answer is: It is the first Gene downstream of basepair-1, then why is basepair-1 at this particular position)

Why the question? Since bacteria show frequently functional synteny between genes, should I be surprised to find a gene frequently associated with the (arbitrary?) annotation origin? If the annotation origin is i.e. the origin of replication that would be an interesting case of synteny, but if no such rule exists, then such a case would most likely just reflect the historic sequence of Genome Sequencing

[I'm sure we have a skilled microbiologist somewhere here, so he would correct my answer.]

The necessity to designate gene locations in classical bacterial model species predated the genomic era, so traditional maps were normally neither bound to origin of replication, nor were they necessarily expressed in base-pairs. In E. coli, for example the traditional map was created based on the F-pili-mediated DNA transfer experiments.

When whole genome sequences became available it was only natural to continue the traditionally defined numeration in terms of placing the "base-pair one". Thus, in E. coli "the traditional and physical maps ... linkage map are closely correlated".

My understanding of the current situation with bacteria without genetic prehistory is that their genomes are numerated either respective to classic closely-related species (if any) or according to the presumed location of ori. Just to give an example of how the dilemma was solved for the Buchnera genome: it was "assumed the DnaA box upstream of the gidA gene is the replication origin" and the authors decided to designate "the start of the DnaA box as base pair one".

As you see, still, even if the authors try to define "base-pair one" based on the position of ori, the problem is that this point depends on the ori-searching tool one uses and on the contemporary understanding of how ori-sites look like (direct determination of origins of replications are in many cases not easy). See e.g. this table with a revision of ori locations in a set of genomes: while most of the genomes received their numeration irrespective of ori, some of them were indeed bound to it, but the new analysis showed that these locations were inaccurate.


How can soft tissue exist in dinosaur fossils? In this article the author explains that they found soft tissues inside of 68-million-year-old dinosaur fossils. How can that be possible? It was believed that soft tissues cannot last more than a million years and that DNA degrades even sooner.

  Our findings challenged everything scientists thought they knew about
  the breakdown of cells and molecules. Test-tube studies of organic
  molecules indicated that proteins should not persist more than a
  million years or so; DNA had an even shorter life span.

What is the evidence that the fossils were real?

keratin and collagen are an incredibly tough molecules so if it is isolated from the environment (oxygen and bacteria) it could easily survive for that long. Not all proteins are equal some are very robust other very fragile. We have long known protein and carbohydrates can survive for incredible lengths of time under the right circumstances, amber is famous for it. Rapid deposition of minerals can produce a similar if less powerful result.

In this case the keratin was encapsulated by water deposited minerals that sealed it away from the outside environment. There are other examples as well, natural mummification can lead to some preservation in the form of biofilms and impressions. But the most dramatic are amber encased specimens. Amber is a quick forming and creates a perfect air seal.

here is a dinosaur tail preserved in amber.


What are the positive and negative effects of insulin on cognitive function? A UCLA study seems to imply that insulin interferes with cognitive function.

  The DHA-deprived rats also developed signs of resistance to insulin, a
  hormone that controls blood sugar and regulates synaptic function in
  the brain. A closer look at the rats' brain tissue suggested that
  insulin had lost much of its power to influence the brain cells.

  "Because insulin can penetrate the blood–brain barrier, the hormone
  may signal neurons to trigger reactions that disrupt learning and
  cause memory loss," Gomez-Pinilla said.

  He suspects that fructose is the culprit behind the DHA-deficient
  rats' brain dysfunction. Eating too much fructose could block
  insulin's ability to regulate how cells use and store sugar for the
  energy required for processing thoughts and emotions.

  "Insulin is important in the body for controlling blood sugar, but it
  may play a different role in the brain, where insulin appears to
  disturb memory and learning," he said. "Our study shows that a
  high-fructose diet harms the brain as well as the body. This is
  something new."

At the same time, increased levels of IGF-1 seems to be implicated in higher level of intelligence. IGF-1 is not the same thing as insulin, but it does seem to have many similar effects.

Diabetes

I've not read about any conclusive evidence for a link between insulin and differential cognitive function, but I have read studies that link type-2 diabetes and impaired cognition (1). I will point out now that this is cross-sectional, so the study only reports associations (i.e. diabetes may not necessarily cause the cognitive impairment).

The study I have mentioned does not conclude that this is caused by raised insulin, but rather the effects on the vascular system (specifically microvascular). They also find a significant interaction between diabetes and smoking status, in the context of cognitive impairment. Again, this seems likely to be the vascular system, rather than insulin levels.

A recent review paper also refers to the links between diabetes and executive function (2), but again makes no reference to insulin as the cause, but rather microvascular changes, hypertension, and other associated traits (again, the causes are not known, these are speculative based on the evidence).

Diabetes may not be the best model for studying this though, as it can be characterized by either high insulin (tolerance), or low insulin (impairment) - therefore the association may not be found this way.

Insulin

In a separate review (this may be the best one for you if you only read one of the papers I've referenced) the author posits that whilst insulin may have a neuroprotective role, it also increases amyloid-Beta metabolism and tau phosphorylation, possibly contributing to Alzheimer's-like pathologies (3). Studies have found that insulin directly improves cognitive performance (4) after infusion of insulin, but the long term effects are less certain - it is unlikely to improve overall health having constantly raised insulin serum levels!

However the link between IGF-1 and improved cognition is less disputed, so you may well be right in thinking that the 'overall' effect of insulin on cognition may be protective, but this may just be a marker of good health overall, which is certainly protective!


found this flying ant like insect in pune, help me identify it? Is it species of wasp or ant or fly? I found it in Pune/India. I need its common name at least.

Here is another photo I managed to take...Found at same place as previous one.

This is not a syrphid. It is a fly in the family Megamerinidae, genus Texara. Very little is known about their biology, and they are rather uncommon.


Could plasmids and conjugation mechanisms be used against antibiotic-resistant bacteria? I'm surprised no one has mentioned something like this.
Plasmids are often exchanged between bacteria, sometimes through conjugation. In particular, conjugation could be considered an "open-port" vulnerability.
Intuitively, there are several schemes that exploit plasmids and bacterial conjugation that could form alternatives to antibiotics:
1: Pwnage by Conjugation
A specially engineered nanoscale capsule or specially rigged bacterial cell is programmed to call out to target bacteria for conjugation. When the conjugation tunnel is opened, the capsule or rigged bacterial cell floods the target bacterium with toxins or malicious RNA designed to sabotage it.
2: Fake Conjugation
A specially designed novel antibiotic contains a conjugation-signaling structure. When a bacterium docks with the antibiotic molecule, the antibiotic irreversibly latches on and tears a massive hole in the bacterium from the inside.
3: Backdoor Plasmids
Plasmids that confer significant advantages are isolated from naturally-occuring bacteria and a special "crash gene" is added to the plasmids. The modified plasmids are implanted back into bacteria that are known to spread them around.
The crash gene's promoter listens for a small set of chemical cues. If it detects a certain threshold of 1 of these cues, it becomes active and sabotages the bacterium. The gene could code for a toxin that specifically damages bacteria. Alternately the promoter could be specifically designed so it never releases the chemical cue, forcing the bacterium to repeatedly produce a garbage produce and waste its resources.
4: Bad Neighbor Plasmid
This might be more difficult to build. A synthetic plasmid encodes 2 products: The first confers a significant benefit to prevent bacteria from discontinuing it through natural selection. The other product is periodically ("randomly") transcribed and vandalizes other plasmids, causing large numbers of nonsense mutations. A set of special markers on the synthetic plasmid protects it from vandalism by its own product. This could silently remove antibiotic resistance from bacterial populations and the bacteria have no way of "knowing" they've been sabotaged until it's too late.

If we assume all of these things could be practically done at least at some point in the future, here are the problems I see with the suggestions, and why they might not work (others may spot additional ones).
1 Translocation of a sabotaging 'agent' via the conjugation apparatus.
This basically already exists, look up the various secretion systems of bacteria. In particular, the Type 6 Secretion System does exactly this (though with a somewhat limited target range).
The first paragraph on wiki summarises:

The type VI secretion system (T6SS) is molecular machine used by a wide range of Gram-negative bacterial species to transport proteins from the interior (cytoplasm or cytosol) of a bacterial cell across the cellular envelope into an adjacent target cell.

The reason this wouldn't work is that bacteria have already evolved to deal with such mechanisms, and one we engineer is unlikely to fare much differently.
You can take it from me (as my PhD concerns exactly this!) that changing what the secretion systems translocate, while possible, is very difficult.
2 Phony conjugation
Antibiotics tend to be small molecules. They bind and dock with enzymes or substrates in order to inhibit some kind of activity typically, e.g. cell wall synthesis in the case of Beta-lactam antibiotics such as penicillin. I'm not sure how you imagine it would "tear a hole in the bacterium" really?
Related to the T6SS, are R-type Pyocins, which are co-opted bacteriophages that sort of do this. It requires no conjugation, and the currently proposed mechanism is that they either deliver a payload of toxins or molecules in to the cell by puncturing the exterior, or they simple create a pore in the membrane causing cellular depolarisation and death. As with phage and antibiotics however, these mechanisms can have resistance evolved against them.

As an additional point, unless you could somehow guarantee that the conjugations were sabotaged or ineffectual in some way, promoting conjugation artificially is almost certainly going to aid the spread of resistance and virulence determinants, actually worsening the situation.

3 A suicide plasmid
It is not trivial to 'confer significant advantages' on a cell. Most plasmids are maintained by amelorating a significant disadvantage that is often supplied artificially, e.g. auxotrophy or antibiotic selection. Given the 'choice' bacteria tend to kick out the plasmids unless they simply cannot afford to live without it. Maintaining the replicon is an expensive process in terms of cellular metabolism and resource utilisation.
'In the wild' the weaponised plasmid would likely not persist long enough to be translocated in to any target of interest in a significant enough proportion to have a real effect. The key is that and of these ideas mentioned cannot simply kill a single target cell, as they will not have an appreciable effect on the population. The bacteria will recombine or straight up remove the plasmid if it's in any way deleterious or even neutral to them, until they've 'corrected' the problem.
Addiction modules and toxin-antitoxin systems are common to see in natural plasmids, as with the other ideas mentioned. Bacteria can recombine out the 'poison' though, and eventually over time lose the plasmids. If the toxin is encoded on the chromosome, it's a little more robust.
4 Bad plasmids
See addiction modules and toxin-antitoxin systems above.
I'm afraid in general I think you're underestimating evolution!


What is the meaning of -//- sign? Does $-//-$ sign between trpR and P indicate separation of the trpR gene from the operon? Or could the sign mean that the trpR gene may be present adjacent or far away from the operon, both the possibilities?

Unlike P and O sequences which are literally joined at their ends, the sequences trpR and P are rather distant. The DNA between them is so long, that the limited space of the page prevents a decent proportional representation. So instead of painting a long line of limited-importance strands, the graphic designer choose to omit the part between slashes.

Note that despite the apparent disconnect possibly suggested by the sign -//-, the intervening DNA is continuous. The sequences trpR and P are still on the same chromosome.


Is there a non-bacterial source of lipopolysacchrides I am wondering if there are any other non-bacterial sources of LPS. To my understanding, lipopolysacchrides (LPS) are components of the outer leaflet of gram-negative bacteria, but are there any other sources of LPS such as fungi?.

Yes, there is.

Lipopolysacchrides have been found in eukaryotes. The most famous example is green algae from Genus Chlorella.

According to Armstrong et al., (2002):

  The lipopolysaccharides (LPS) are ubiquitous components of the outer leaflet of the outer membrane of all gram-negative bacteria and are the principal toxic products of these organisms (1). The membrane anchor of LPS is lipid A, a central phosphodisaccharide unit that is attached to multiple -hydroxy fatty acid chains. LPS also contains the novel sugar, 3-deoxy-D-mannooctulosonic acid (KDO). Although generally believed to be restricted to prokaryotes, specifically the gram-negative eubacteria and the cyanobacteria (2), an LPS-like molecule has recently been reported from a eukaryote, the green alga Chlorella sp., strain NC64A. (emphases mine)

Also, for further discussion on LPS in eukaryotes, please see Histochemical Evidence for Lipopolysaccharide (Endotoxin) in Eukaryotes.

Source:

Armstrong, P., Armstrong, M., Pardy, R., Child, A. and Wainwright, N. (2002). Immunohistochemical Demonstration of a Lipopolysaccharide in the Cell Wall of a Eukaryote, the Green Alga, Chlorella. The Biological Bulletin, 203(2), pp.203-204.


How do two parents, recessive and dominant genes and two complimentary nucleotides end up in one DNA? In the basic school, I was taught that half of genome is received from father and another half comes from mother in the form of double-helix DNA, whose first helix consists of dominant nucleotide bases and second helix is a kinda inverted copy of the first helix. I feel like 3 different concepts are mixed here into one DNA spiral and I cannot sort them out. Can you explain exactly how is every concept (parent material, recessive genes and complemenrary nucleotides) are represented in the DNA? The professional and wikipedia explanations are too full and I cannot extract this basic information from too much detail.

For instance, mother and father could donate non-overlapping sections of the double helix, e.g. you inherit a head of DNA from father and tail from mother. I can also guess that first helix consists of primary nucleotides whereas second helix is complimentary. I also understand that despite it is natural think that primary = dominant whereas complimentary nucleotide stands for recessive, it is unlikely coz dominant is a full gene rather than a single nucleotide and dominant is independent and can differ from recessive whereas complemntary implies deterministic relationship between two. Furthermore, receiving dominant from parent1 and recessive from parent2 contradicts the fact that only one of the parent alleles enters the offspring DNA. Probably both are inherited and only one is expressed in phenotype but I am not sure and ask to clarify this. In other words, I would like to know how both parent1 and parent2 chromosomes live in the child DNA if not in the form for helix1 + helix2. Particularly, what are these two chromosomes, next to every person, if not two helix of one DNA

and where are they located? Are these just two DNAs which exist only during meiosis, during first moments of fertilization? How do you end up with only one DNA in the end?

I would also like to know if individual's eggs DNA is coming from his own DNA or is formed in parallel, from his parents' DNA? That is, when individual's eggs' DNA is produced: during fetation of the parent, during his lifetime from his DNA or during fetation of the child?

I think you really need to go back to the very basics and try to understand the DNA molecule, what a chromosome is, DNA replication and mitosis, what homologous chromosomes are, what non homologous chromosomes are, what sister chromatids are, what non sister chromatids are before you attempt to understand meioses. And I would definitely recommend you learn all of these things well before you attempt to understand molecular inheritance, but let me see if I can at least begin to clarify some of your misconceptions.

If you are having a hard time understanding the concepts as written, try looking up the articles on Simple English Wikipedia first. The try to make their articles easier for novices to understand.

There is no such concept as Dominant Nucleotide Bases. The two strands of the DNA double helix are complementary and antiparallel. Genes can reside on either strand.

You are also getting really mixed about recombination via crossing over in meiosis. The chromosomes that are being recombined in the mother are from her parents, so technically the chromosomes that are being recombined are the grandparents chromosomes.

The same is happening when the father produces gametes. The chromosomes from his parents are swapping pieces of DNA.

At the end of meiosis, each gamete has a random assortment of 23 chromosomes, either from the father or the mother of the adult male or the father or the mother of the adult female.

The 23 can be recombined meaning that the chromosome is part grandma and part grandpa, or it is a grandmother's chromosome that has not recombined or a grandfather's chromosome that has not recombined. Just looking at the possible ways that 23 chromosomes can randomly assort without taking into account recombination to produce a gamete, there are about 8 million combinations. Add recombination and it gives you a huge amount of genetic diversity.

So those are the haploid gametes. When fertilization occurs the sperm from the father donates its random assortment of 23 chromosomes and the ovum from the mother has 23 randomly assorted chromosomes of its own. This gives you at total of 46; 23 from the father, made up of a random assortment of chromosomes from his father and mother (or chromosomes recombined by crossing over to be part his mom and part his dad), and 23 from the mother with the same pattern of random assortment and recombination.

Also, the double helix doesn't dissociate (come apart) during crossing over [NOTE: for those who know, please do not jump on me for not explaining strand invasion here and the need for homologous sequences for crossing over]. One part of a grandparent's chromosome is exchanged for the exact same part of a chromosome from the other grandparent's chromosome, assuming normal cross over events. The alleles (versions) of the genes in that segment may vary, which is why you have a chromosome is part grandmother and part grandfather.

As for dominant autosomal genetic traits versus recessive genetic traits. A dominant trait means that a heterozygous child will express the phenotype even though they only have one copy of the dominant allele. If it is a disease, then we say the person is affected. If it is a recessive trait, then the heterozygous child will not express the phenotype, so they are not affected by the disease, but they carry the allele and can pass it on to their children. This person is said to be a carrier. If a person is homozygous for a recessive trait, then they will be affected by the disease and show the phenotype.

As for inheritance, you have to draw the punnet squares. This will show you the different patterns and probabilities of inheritance.

UPDATE

I think that you are getting confused by the idea that you inherit one set of 23 chromosomes from your mother and one set of 23 chromosomes from you father. While this is true, meiosis happens in their reproductive organs before fertilization (for the most part, but the important part happens there and then).

The example of the father is easier. He has two sets of chromosomes, one set that he inherited from his mother and one set he inherited from his father. At the beginning of meiosis all 46 chromosomes replicate. They make an exact copy of themselves and are joined at the centromeres. You have 2 sister chromatids on each of those chromosomes. Now the the homologous chromosomes will pair up, so one of the chromatids on the paternal chromosome (say chromosome 4 from Grandfather's set) will join with a non sister chromatid from the maternal chromosome (Grandmother's chromosome 4). So you have four chromatids from chromosome 4 lined up at the metaphase plate. The two non sister chromatids that are joined will recombine when the kinetochores move along the microtubules towards the poles of the spindle. At the end of all of this you have two cells that contain 23 chromosomes, each with a sister chromatid, however the sister chromatids are no longer identical because one of them recombined with the the non sister chromatid of its homologous chromosome. The thing you must remember is that each chromosome assorted independently of the other. For Chromosome 1 the maternal chromosome may have gone to the left cell while the paternal chromosome went to the right. Then for chromosome 2 you might have the maternal chromosome go right and the paternal chromosome go left. And so on and so forth. The number of possible combinations of how you can arrange two sets of 23 chromosomes is 2^23 or about 8 million different combinations.

During meiosis II the 23 chromosomes again line up at the metaphase plate and they are attached to the spindle by both sides of their centromere / kinetochore complex. When the migrate the two sister chromatids migrate towards opposite poles. Again it is completely random as to whether the recombined chromatid or the chromatid that did not undergo recombination will migrate to the right or the left. Again, there are 2^23 possible combinations for EACH cell.

So you end up with an incredible amount of genetic diversity on how chromosomes are assorted within the gametes. You will still only have four possible outcomes  in the copies of any single gene that you get. You will inherit either your paternal grandfather's copy or your paternal grandmother's copy and you will inherit either your maternal grandmother's copy or your maternal grandfather's copy. That is why if a genetic disease is caused by one gene, it depends on which copies you inherit.


Apolipoprotein B48 and fat storage Can chylomicrons formed in the intestine, with apolipoprotein B48, transport lipids to adipose cells for storage?

Fatty acids originating from  chylomicron  triacylglycerol  are delivered mainly  to  adipose  tissue,  heart, and muscle (80%), while ~20% goes to  the liver. - source: Harper's illustrated biochemistry.

Lipoprotein lipase which is present in wall of blood capillaries anchored to endothelium by negatively charged proteoglycan chains of heparin sulfate requires phospholipids and apoC2 for its activity to take place.

Hydrolysis takes place while the lipoproteins are attached to  the enzyme on  the endothelium. Triacylglycerol  is hydrolyzed progressively through a diacylglycerol  to  a monoacylglycerol  and finally to  FFA plus glycerol with the help of lipoprotein lipase.  Some of the released free fatty acid return to general circulation bound to albumin but the bulk is transferred to peripheral tissues like adipose tissue, muscles of heart etc.

Fate of chylomicron
The lipase activity results in loss of 70%-90% of triacylglycerols and apoC2.(source: Harper's illustrated biochemistry) The remnant chylomicron is then taken up by liver by receptor mediated endocytosis. Here cholesteryl esters (present in concentrated form after loss of most of triacylglycerol) and remaining triacylglycerols are hydrolysed and metabolised.


What is the distinction between F' plasmid and R plasmid? Is there a difference between an F' plasmid that has taken up a chromosomal gene that conveys antibiotic resistance, and an R plasmid? Is a bacterium containing an R plasmid and yet lacking an F+ plasmid capable of horizontal gene transfer by conjugation?

If I understand the nomenclature correctly, an R plasmid is just any plasmid containing an antibiotic (R)esistance gene (eg. Amp, Kan, Cm, etc.). It's a bit of an outdated name from when people didn't know how exactly the plasmids conferred such resistance.

An F-plasmid is any plasmid that contains the genes necessary for (F)ertility, eg:horizontal gene transfer via the tra operon.

The two do not have to appear together -- eg: Many F plamids will contain resistance genes (along with other random chunks from the genome), but resistance doesn't always have to be part of the payload. Likewise, it is common in labs to build pure resistance vectors that lack any horizontal transfer capability in order to select for particular clones.