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How does a blunt force stimulate histamine to develop early stages of inflammation?
I know that viruses and sharp forces can stimulate mast cells by cut or by a virus infecting them and then release histamine. How can blunt force do this and cause inflammation? It doesn't have the above process. And how will the macrophages, neutrophils and plasma cells  react to this type of inflammation when there is no bacteria or viruses to swallow and create antibodies for?

An brunt force (trauma) may destroy cells and tissues by mechanical action. It simply squashes them.
Cells contain different kinds of chemical substances in specific cellular organelles. The most important in this context are enzymes from lysozyme.
Once enzymes are released (by squashing the cell) they induce irritating reactions to other cells and activate specific receptors found on immunitary system cells. This is how non-infectious inflammation occurs.
Cell components act as inflammatory mediators responsible for the clinical signs of inflammation. Here are some examples  [Wikipedia]:

Lysosome granules from destroyed cells
NO (Nitric oxide) from endothelial cells and some neurons

Other inflammatory mediators are produced by macrophages, neutrophiles and plasma cells, thus leading to a chain reaction, in which immunitary system cells activate one by another.
Macrophages have enough to 'swallow': all the destroyed cells which must be removed from the tissue.
Antibodies are produced because altered cell structures are considered non-self and gain antigen properties.
Source: Wikipedia, Inflammation


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Do insects respond to the detection of dead insects?
Are there insects that change their behavior upon detecting the nearby presence of other dead insects? If there are, can you provide an example?

Yes, it is a common behaviour and is called necromone signaling (Yao et al 2009, see references in paper for many examples), and is probably used to avoid predators, parasites and disease. The chemicals used are often similar (unsaturated fatty acids), and seem to have an old evolutionary history (~400 million years). Many groups of species can also detect infected, not yet dead, conspecifics. Removal of dead individual is also common in e.g. ants (necrophoric behavior).
The paper referred to earlier (beside reviewing earlier evidence) also provides experiments of detection/avoidence in isopods and Tent
caterpillars (Malacosoma americanum), where they show avoidance based on crushed conspecifics, unsaturated fatty acids and (for isopods) intact corpses.
Naturally, the same type of compounds are used by e.g. species of carrion beetles (Silphidae) to find their animal hosts, but then for the purpose of reproduction.

Ants respond by eating the dead insect, except if it is one of their own, most of the time.

True. I originally read the questions as asking about detection of dead individuals of the same species, but I now see that this is not entirely clear.

The experiment where a live ant is 'painted' with necromones is one of my favorites. The painted ant is repeatedly carried out of the nest (and will aid other workers in carrying itself), and then walks back into the nest.

source: Stack Exchange

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sort: votes


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Why is coconut oil healthier when it has so much saturated fat?
I noticed that coconut oil has ~96% saturated fat, and I was under the assumption that saturated fats = bad for health.
Why is it that coconut oil is healthier to alternatives with much less saturated fat?

coconut oil is composed mainly of medium-chain triglycerides, 1)it is smaller than other long-chain triglycerides so that it can be digested easily, 2)the digestion of coconut oil does not involve in the Pancreatic digestive enzyme system, 3) liver prefer use medium-chain triglycerides as the fuel sources 4) medium-chain triglycerides will convert to monoglyceride and medium-chain fatty acid which have strong antibacterial

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Do animals exist with an uneven total number of digits?
I recently finished reading Contact by Carl Sagan. In the book they talk about a pattern in the transcendental number like pi or e, and comment that it is found in base 10 or however many fingers the race has to count with.
When in the end they find a pattern in pi it is in base 11, which I found a strange choice since I can't think of an animal that has an uneven total number of fingers, and I would think that most evolution would result in a somewhat symmetrical design.
Do any animal exist that has an uneven total number of fingers or equal lim, excluding polydactyly and oligodactyly?

I had a quick look around and I cant see any actual proof that pi has a pattern in base 11 apart from that book ?

The pattern is a fictional part of the book, but the author based a lot of the information in the book on existing scientific knowledge. There for i found it strange that he chose base 11, and I wanted to know if there where some beings on earth that if they where the dominant spice could have evolved to count on an uneven number of lims, but as Brandon pointed out some count in other ways.

cf. http://math.stackexchange.com/questions/460729/what-would-have-been-our-number-system-if-humans-had-more-than-10-fingers-try-t

Coscinasterias calamaria, the Eleven-Armed Sea Star! (Although I doubt it has much to do with pi)

Image from Wikimedia Commons

although both C.calamaria and "pi" sound similarly delcious

Thanks for the answer, hadn't considered that, now can you teach them to count ;)

This has 11 votes, so I refuse to add another. sorry.

this is a good answer since bilateral symmetry is what creates even numbers of digits.

Maybe tube feet are more equivalent to "digits"? Although if you define fingers as "things you open yummy mussels with", sea star arms pass the test.

@ghoppe:  others have brought the total above 11.

The key point here is the radial body design, not whether the arm of a starfish counts as a digit. One could imagine some alien life form with a radial body design of 5 "arms" and 5 "digits" or fingers on each arm. Those would then be true digits and the total count would be 25 - still odd.

I just wanted to say that I believe you're seeing it from a quite anthropocentric standpoint. It doesn't make much sense to search for patterns like even or odd numbers of fingers or limbs.
If evolutionary tends to result in bilateral symmetry, there is no reason at all why the symmetry should be inconsistent - like 4 fingers on one hand and 5 on the other.
Consistent bilateral symmetry will always result in even numbers:

4 fingers x2 = 8
7 ribs x2 = 14
5 toes x2 = 10

The Eleven Armed Sea Star in @Oreotrephes' answer isn't much of an exception to the rule of symmetry, it's just radially symmetric.


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Reflexes & Pathologies including the Vagus Nerve
I only know the vasovagal reflex. I would really appreciate if someone could inform me about the other ones.
About the pathologies, I already know the effects of direct nerve damage. I am talking about more sparse and indirect ones, for example so far I found Roemheld syndrome, which is a gastrocardiac syndrome.
Actually, any subtle clinical presentation including the vagus nerve could be really helpful!

One pathology affecting the vagus nerve is autonomic neuropathy which can be secondary to several causes-one of the most commonly acquired cause is diabetes mellitus. It can manifest with various symptoms such as resting tachycardia (heart beating fast without exercise), exercise intolerance, orthostatic hypotension, constipation, gastroparesis (delayed gastric emptying), etc.
If you'd like to read more-http://care.diabetesjournals.org/content/26/5/1553.full
Hope its helpful.

I know the vagus nerve is linked to ulcerative colitis, which could have serious effects on the brain due to body-wide inflammation. You could probably search "vagus nerve" "colitis" and "neuroinflammation" and get some good papers on pubmed.


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Is there any possibility of interspecies sexual reproduction in animals like hybridizing plants?
Inter-species sexuals are happening naturally. My questions is, whether it may lead a creation of new species? This question arises, because of the appearance of Pillayar in hinduism. Please clarify, whether it is possible to create a new species with the appearance of "Vinayagar" that is human body with elephant face.

You might explain what Pillayar and Vinayagar are, for the benefit of those who aren't that familiar with Hindu culture.  But closely-related species can produce offspring: mules, wolf-dog,coyote-dog, and coyote-wolf hybrids, ligers and tigons, "beefalo" (cow-buffalo), and more.

The answer is : A big NO.
Naturally, there is no way possible to create a species like vinayagar. Humans and elephants are totally different, they belong to totally different orders. And success rate of inter-species reproduction is rare for even species from same family but from different genus.


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Standard curve for real time
When performing a standard curve for some new primers to test for fold change, is it necessary to run the standard curve? I mean, in case your experiment has several genotypes for the same ecotype background, with correspondent control and treatments, must I run the standard curves for all this scenarios, or rather may I pick, just to say a random genotype of treated ones, see that it R=0.99 is or higher and efficiency 2?
It is in order to not to waste material.

Do the standard curve once for each primer pair to determine efficiencies. You can use the efficiency values for any number of replicates with any template.
I think we have somewhat discussed this issue in your previous post.

sorry to disturb but then if i get an efficiency value using control tissue, this values may be used for treatments, isn´t it?

yep.. the efficiency is just the property of the primer and its template DNA..


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How did aquatic dinosaurs go extinct?
Dominant theory is that 'normal' dinosaurs went extinct from ether super volcano or meteor impact or combination of both. However there were aquatic dinosaurs that are not present at this day. Was it one of the events above that caused them to go extinct, or was it something else?
How did aquatic dinosaurs go extinct?

There is a very good answere here, which lists the reasons and the species that you asked about. https://www.reddit.com/r/askscience/comments/1nyuqs/what_caused_all_the_giant_underwater_reptiles_to/ Mososaurs and pliosaurs were technically giant reptiles, 10 meters long. Alligators and Tortoises are marine and they were the only surviving sea-reptiles. the KT extinction killed many tropical corals and ecosystems according to fossil records.

Spinosaurs (like Spinosaurus) are currently only known from 112-97 million years ago, although isolated teeth push the origin possibly back to ~150 Mya. At least now, there isn't any definite spinosaur material younger than 97 Mya.
So spinosaurs were already extinct when the rest of the non-bird dinosaurs went extinct at the end of the Cretaceous, whether by meteor impact, volcanism, a combination, or something else completely.

keep in mind spinosaurus is also nowhere near fully aquatic.

Spinosaurs and ichtiosaurs dissapeared before a great anoxic event at 90Ma. What about pliosaurs, they are reptiles strictly speaking, 10 12 meters long, fully marine, that vanished at the KT boundary. en.wikipedia.org/wiki/Plesiosauria and mososaurs.

Not a lot of people realize how extreme and how sudden the dinosaur's extinction was. Radiolab did an episode with several geologists about the extinction of the dinosaurs. Basically, when the meteor hit the Earth, a humongous amount of material was ejected into space, and most of it fell back down to the surface all around the planet. As it fell it left an incredible amount of heat in the air, raising temperatures to as high as 1200 Farenheit (650 Celsius). Anything too large to hide under dirt died (dirt is a surprisingly good insulator). Even plankton and animals near the surface of the ocean would have been decimated by the heat, destroying the food chain that supported the large mesosaurs and plesiosaurs. The whole process is thought to have taken 2 hours. The fact that anything lived through that at all is dumb luck, and even if a semi-aquatic dinosaur was deep enough to avoid the worst of the heat, the food supply would have been destroyed and they would have starved shortly after the impact.

Interesting info, but the aquatic dinosaurs went extinct millions of years before the meteor. So, this doesn't answer the question.

@rumtscho Mosasaurs didn't go extinct until the end of the cretaceous. Some plesiosaurs did too. While these are technically not dinosaurs, for all practical purposes they are close enough, and a lot more aquatic than spinosaurus ever was.

now that I read the question again, I may have misunderstood it. I have to make a pro forma edit before I can remove the downvote. But I have to wait for the peer review.


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Why does botulinum toxin seem to be more dangerous to humans than to other mammals?
Various mammals seem to get away with eating parts of carcasses that we would prefer to not even touch, and that we assume will make us sick.
Because of that, I assume botulinum toxin is more dangerous to humans than many animals.
Is that right so far - can they handle more of some toxins compared to us?
Or are they better in avoiding harmful substances based on more suited olfactory sense?
Or are we just more afraid?
Assuming the differences exist - what is the cause for it?
Are there plausible explanations in terms of evolutionary pressure?

How do you come to the conclusion that is is more dangerous for us? Botulinus is a strict anaerobic bacteria, so you will not likely find it on relatively fresh carcasses.

Humans have a tendency to can things and put food in jars, which is more or less a recipe for botulism. Vultures have a huge list of fascinating adaptations for eating rotting carcasses but that's an answer for a different question.

@Chris Yeah, I was not that sure with it - that's why I called it assumption. So part of it is the "Or are we just more afraid?"... And right, the vultures deserve a separate question!

@JeremyKemball makes sense, the fact that most other animals never tried to keep a carcasse until next summer seems to be important, worth making it answer.

It's an interesting question other than your assumption about botulinum toxin, which is incorrect and seemingly irrelevant. Perhaps you should remove it. http://www.sciencedirect.com/science/article/pii/S0300908400002169?via=ihub#TABI

From a food safety point of view, you don't get botulism from "carcasses" (meat). Common botulism vectors are plants, especially the parts growing around dirt (making homemade garlic oil is a really bad idea), and honey (a danger to infants, adults can stomach the spores and they can't form a colony of living bacteria in honey). So, if there are animals which come frequently into contact with botulism, they aren't vultures. Actually, I might have to write an answer about that...

Because of that, I assume botulinum toxin is more dangerous to humans than many animals.

Couldn't find too many examples but, there are some things to consider (according to [1]):

there are seven distinct types of toxin with variable action among animals
different dose / effect intensity ratio between toxin types
toxins A, B, E and F cause disease in humans
toxin C and D are more common to birds, cattle, horses

And here are some numbers:

cattle median lethal dose: 0.388 ng /kg [2] of C type toxin
mouse median lethal dose ( 12.88 times more than cattle): 5 ng/kg [2] of C type toxin
human median lethal dose: 1 ng/kg [1] of A type toxin

When it comes to carcasses toxicity, there are some papers to consider:

Smith GR, Turner A. Factors affecting the toxicity of rotting carcasses containing Clostridium botulinum type C. Epidemiol. Infect. 1987 Jun;98(3):345-51. PubMed PMID: 3297745. - Persistent toxicity at 20 and 37 degrees Celsius even for a long time. No toxicity at 16 degrees Celsius
Smith GR, Turner A, Till D. Factors affecting the toxicity of rotting carcasses containing Clostridium botulinum type E. Epidemiol. Infect. 1988 Jun;100(3):399-405. PubMed PMID: 3288491. - Maximal toxicity at 30 degrees Celsius that is lost in time.

are they better in avoiding harmful substances based on more suited olfactory sense?

Not if we are talking about nonproteolytic B, E and F type bacteria. Indeed, Clostridium botulinum, proteolytic type A, B and F types produce odor [3].

Or are we just more afraid?

I don't see how fear could (significantly) influence pharmacodynamics and pharmacokinetics of the toxin.

References:

CIDRAP - Center for Infectious Disease Research and Policy. Botulism. Available from http://www.cidrap.umn.edu/infectious-disease-topics/botulism
Moeller RB, Puschner B, Walker RL, Rocke T, Galey FD, Cullor JS, Ardans AA. Determination of the median toxic dose of type C botulinum toxin in lactating dairy cows. J. Vet. Diagn. Invest. 2003 Nov;15(6):523-6. PubMed PMID: 14667014.
P. Kendall. Botulism. Colorado State University Extension. Available from http://www.ext.colostate.edu/pubs/foodnut/09305.html

I think he means 'fear' in the sense that humans worry about botulism, and vultures apparently do not. Some explanations: vultures are less affected by botulinum toxin, vultures aren't exposed, and vultures just don't worry about things. Seems to be a blend of 2 and 3, but it's interesting to point out that in certain temperature/time windows carcasses might be poisonous to humans but not to vultures, due to differences in relative toxicity/toxin type. A faulty assumption is sometimes right.

You seem to not understand how botulism works. It is impossible for vultures (or anybody else) to get botulism from a carcass.
First, you have spores. They are ubiquitous in nature, and you have probably eaten lots of them. They are especially common on vegetables growing around/in dirt, like garlic. The spores are

indestructible when using common cooking methods
dormant under normal food storage conditions
not dangerous to humans above 1 year of age. They remain dormant in the human body and get excreted without causing anything.

Then, you have botulinum bacteria colonies. To get a colony going, you need to take some spores and cut off the oxygen supply. For example, storing raw garlic in oil provides both a possible contamination route and a perfect growth environment.
The bacteria themselves are
  - easy to kill off with heat
  - not prone to establishing a colony in your body.
The problem with the bacteria: Once there has been a colony, it starts producing the toxin. This toxin is very poisonous even in minute amounts, and stays around to harm you even after you have killed the bacteria which produced it (e.g. with acid). It is not especially heat stable, certainly not as stable as the spores.
So, the way you get botulism is:

Start out with food contaminated by the spores (meat is rarely such food, vegetables are more common. Of course, cross contamination in your kitchen is possible.)
Cut off all oxygen supply for some time. A colony forms.
Sterilizing the food by placing it in boiling water for some time doesn't matter, the spores will survive it easily. (This is why industrial food is canned at much higher temperatures, and safe home canning recipes are quite acidic).
eat the food after it has been stored with the colony inside.

So, vultures don't have any special resistance to botulism toxin, they just don't come in contact with it.
On a side note, there are quite a few other pathogens which are common in meat, and vultures are probably more resistant to them than humans. But it is normal for bacteria to be able to only make one species, or a small range of species sick. Just ask the poor medical researchers trying to heal human disease in mouse models - there are huge differences.


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identification of species of this bird
Hi I saw this bird near my school canteen in Singapore in Spring. Can anyone identify the species of this bird? Thanks in advance!

Can you add the geographic location where it was found and the time of year?

@kmm: Singapore, and recently, a few days ago.

I would say that it would be a subspecies of a raven or a crow but it is hard to identify seeing that the bird has been through a disease or met with an accident..

This question may be difficult, but it isn't too broad. In fact, I can't imagine a narrower question than "Which species is this animal?". I think that the question should be reopened.

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Can we remove impacted teeth by key hole surgery?
Can we remove impacted teeth by key hole surgery, rather than an open technique, like lithotripsy?

Could you add some additional context to your question, such as what you know, why you are interested, etc.? It's not clear what you are seeking beyond a yes or no answer.

The impacted tooth is partially or fully enclosed in the bone. Even if accessed by a drill hole to reach the tooth. The tooth is too hard to be cut up into smaller sections with any of the conventional equipments available through an endoscope.
Tooth is a composite of three highly organized, mineralised tissues. The bulk of the tooth is formed by dentin and has around 30% organic content almost similar to that of bone. A large part of the organic content is collagen a tough fibre. Where as kidney stones etc are aggregates of minerals etc and are much more susceptible for pulverisation by shock waves from a lithotripter.
Besides an impacted tooth is either partially of fully inclosed in bone. So that too rules out the use of a lithotripter.


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Cloning two fluorescent proteins with different promoters in the same plasmid?
I want to clone two fluorescent proteins both driven by different promoters in a plasmid to be used to transform B. subtilis at the amyE locus. For this I want to use plasmid pSG1729 (Lewis and Marston, 1999), because this plasmid can be used for homologous recombination at this specific locus.
Now the problem is, because of a few reasons (i.e., the locations of the restriction sites, keeping the spc resistance gene and deleting the current GFP gene), if I want to clone two genes into this plasmid, they will be very close to each other (~10bp). Will this be a problem either technically or biologically after transformation? I don't think that possible read-through will be bad, as I want one of the fluorescent proteins (pHluorin) to be continuously expressed. Maybe an option would be to clone the two genes in opposite directions?
This is the current genotype of the plasmid:
Ori amyE5' currentGFP Spc amyE3' bla

you can use bidirectional promoteror you may extend the spacer to ~100bp just use the 10bp spacer in tandem or better, with some reshuffling..

The spacer is a good idea, can you maybe elaborate on the reshuffling?

just use similar sequence but not exactly the same sequence.. you can move some bases here and there.. though, not really essential to do so, it will reduce repeats..

If you want to express them in an operon, make sure you have an RBS at the 5' end of each coding sequence. If you place one 10bp downstream without it having an RBS, it will be transcribed, but not translated... If you want more help, paste the DNA code of each as a comment.


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In the context of twin studies, what do 'unique environmental factors' and 'shared environmental factors' refer to?
I was reading this study on sexual behavior and they refer to both terms without clarification. Does 'unique environmental factors' refer only to the prenatal environment or does it include individual experiences with, say, illness as well? Would friends be considered a 'shared environment factor' or an 'individual environment factor?'

Shared environmental factors are those shared by the twins: uterine/prenatal environment and then the home environment and other environments both twins are raised in or remain in together. Unique environments are any environment not shared by the twins - they generally appear later in age.


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Suitable introductory book on Bioinformatics for a computer scientist?
Do you have any suggestions on a suitable introductory text on bioinformatics for a computer scientist? Any recommendations with pros and cons of different books would be appreciated. I'm mainly looking for a brief introduction since I'm a novice to this field.
I found some books like

Systems Biology by Edda Klipp,
Introduction to Bioinformatics  by Arthur Lesk
Bioinformatics For Dummies
Bioinformatics and Functional Genomics by Jonathan Pevsner
An Introduction to Bioinformatics Algorithms by Neil C. Jones and Pavel A. Pevzner

I would like to develop software related to sequencing applications, so any suggestions should ideally aid in this goal.

Can you narrow down your requirements any, as I think this is too broad to get a reasonable answer.

I was looking for something related to sequencing, Since looking for developing software for it

I would put as much information as possible into the question itself.  Asking for the "best" book is going to get a host of opinion-based answers.

With a slightly reformulated Q I do not see a big problem - BioSE has many open questions about book suggestions. Adding specifics about future software development and therefore need for technical aspects of sequencing would probably be useful though.

@fileunderwater why did you remove one of the books from the OP's list?

@terdon Mistake on my part or the Q was updated while I edited. Maybe a mod can put it back in.

@fileunderwater no worries, I put it back. I was just asking in case there was a valid reason.

I added the bit from your comment - I think it's an important point that actually narrows the books under consideration.  Please edit it as you would like, but I'd encourage you to put specific information into the question directly as @jonsca suggested, since few people are going to read this long comments section.

"Biological Sequence Analysis" by Durbin et al. is the classic bioinformatics text for people with a CS background. If you are interested in a more quantitative approach to biology without necessarily focusing on algorithms, you will also probably find "An Introduction to Systems Biology" by Uri Alon and "Physical Biology of the Cell" by Phillips et al. interesting (depending on your area of interest). Additionally, any Machine Learning text will be relevant and some often have examples from biology/bioinformatics.

@Bitwise I've reopened the question now, could you please create an answer from your comment.

Systems biology and bioinformatics are quite diverse subjects, but here are some options:

Biological Sequence Analysis by Durbin et al.: the classic bioinformatics text for people with a CS background. Does not deal with networks.
An Introduction to Systems Biology by Uri Alon: A physicist's view of systems biology, focusing on design principles and networks. Interesting concepts and some math (no algorithms). Doesn't really deal with methodology.
Physical Biology of the Cell by Phillips et al.: Nice introduction to biophysics and quantitative biology (no algorithms). Many parts are relevant for systems biology.
Any diverse Machine Learning text will be relevant and many have examples from biology/bioinformatics.
Probabilistic Graphical Models are also quite popular in bioinformatics (e.g. Hidden Markov Models, Expectation-Maximization, Bayesian Networks). Probabilistic Graphical Models by Koller et al. is a very comprehensive CS book on the subject.

Another suggestion is to look for primers/reviews in relevant journals. This is important because the field is new, so once a new technology is developed, it takes time until the appropriate computational methodology is developed enough to make it into a text book. Also, they can point you to relevant research papers. For example, PLoS Computational Biology has an Education Collection which features a large variety of such reviews.

For a really brief introduction, I recommend the 37 page paper
Bioinformatics - An Introduction for Computer Scientists by Jacques Cohen.
It is a well written text, assuming some knowledge about algorithms, computing and maths, but not about biology. It helped me a lot getting comfortable with the field.
Afterwards, I'd stick to Durbin's "Biological Sequnce Analysis" (as already mentioned by Bitwise) as a book that provides you with the theoretical foundations of the models used in bioinformatics. It focuses on Sequence processing, which is what you want as far as I understood your question. It is also quite accessible from a computer scientist's or mathematician's point of view.

I second these two I used both and liked them overall:

Bioinformatics and Functional Genomics by Jonathan Pevsner
An Introduction to Bioinformatics Algorithms by Neil C. Jones and Pavel A. Pevzner

For my bioinformatics class a few years ago, we used these:

Fundamental Concepts of Bioinformatics - Krane and Raymer

Was excellent as an intro text. Explained a lot of the biological concepts while it was teaching you the methods. Useful either for biologists or computer scientists bridging into bioinformatics.

Statistical Methods in Bioinformatics - Ewens and Grant

The go to book for more comprehensive coverage of algorithms and applications. Did a good job covering the details of a method, like dynamic programming, from start to finish.  Much more computer science oriented.

There several popular books for bioinformatic

A First Course In Computers 2003 Edition (With Cd)
Foundations of Computing (English, Paperback, Sinhs Pradeep K.)
Introduction to Bioinformatics
Bioinformatics: Methods and Applications: Genomics, Proteomics and Drug Discovery by S. C. Rastogi
Bioinformatics: Concepts, Skills & Applications
Principles of Genome Analysis and Genomics

You can find the list of bioinformatic books here 6 Best Books for Bioinformatics

Welcome to Biology.SE. Please take the [tour] and carefully read through the [help] to learn more about the site, including what is on-topic and what is not, and [answer] questions. In particular, note that this question was not appropriate for this site because it solicits opinions and so should not be answered — from [answer], Answer well-asked questions. Not all questions can or should be answered here. Note: You may find [bioinformatics.se] to be of interest. Thanks!


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Why can't we observe haplotypes directly?
I am completely a noob to biology and DNAs, but recently I am looking into EM-algorithm used in the case of re-constructing haplotypes from genotype data.
I am just wondering what exactly in the process of DNA data collection prevents us from observing haplotypes directly.

I am not completely sure what you mean. In DNA extraction, not even chromosomes are (usually, it is sometimes possible) singled, much less alleles. You have a complete bunch of chromosomes that you shear, most of the time put through PCR, tag with adapters and sequence. Often you actually even sequence several different probes together, so you additionally add a barcode to sort them afterwards. There are sequencing errors and different alleles and you have to figure out which read belongs where ... but this would be an answer, not a comment. Is this what you want to know more about?

To fix the problems that @skymninge pointed out EM (Expectation maximization) algorithms are used which try to find the likelihood of a read arising from a location

The difficulty of reading haplotypes 'directly' lies in the difficulty of reading any long sequence of DNA, and this is for technical reasons.
Short DNA fragments are sequenced using a variety of methods. Gel electrophoresis can pull these fragments apart by length, but all the fragments have to be relatively close in size to get the accuracy needed to tell fragments that differ by one base pair apart. It's easy to separate a 16-bp segment from a 17bp segment easily, but it's much harder with a 516bp segment and a 517bp segment. Modern sequencing can sequence reads up to about 5kbp in length at a time. The 'reads' are then reassembled.
There are next-generation methods(pyrosequencing, etc) that can read a long dna molecule one base at a time, but for practical reasons sequencing an entire chromosome this way is cost and time prohibitive. As a result, there are always going to be fragments that you need to reassemble computationally, no matter how the sequencing is done.

Are you asking why it is difficult to tell whether a cell is homozygous or heterozygous? If so, this is usually a combination of sensitivity of the assay (rtPCR can be optimized for this purpose - at least, I've heard of people doing it). Another aspect of this is that even if the alleles code for different things (eye pigment or something), much of the gene may be similar enough that PCR primers are difficult to construct in a way that they distinguish between the two alleles.
Then again, sometimes you get lucky and there's an EcoRI site right in the middle of one allele, but not the other.


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How does ubiquitin recognize misfolded proteins?
Misfolded proteins are tagged by ubiquitin and then are destroyed by proteasomes. How does ubiquitin know which protein to tag?

http://www.youtube.com/watch?v=hvNJ3yWZQbE I think this video explains the ubiquitin system very well.

Ubiquitin and the UPS
The ubiquitin proteasomal system (UPS) is a common method of regulation for many proteins in the cell. The modification is actually generated by E3 ubiquitin ligase, of which there are ~400-800 in the mammalian cell and the main source of specificity in the UPS (E2 ~40 and only 1 or 2 E1).
Ubiquitin gets its name from ubiquitous, meaning found everywhere. It's a 76 amino acid molecule that modifies proteins at lysine residues. Monoubiquitination can act as a signalling molecule whereas polyubiquitination leads to degradation. Ubiquitin is first activated via an ATP-dependent pathway to create a high energy thioester with E1. This is transthiolated to E2 and finally E3 allows the addition to the target protein. So really, your question is how E3 ubiquitin ligase recognises its target. 1
E3 ligases
There are 3 classes of E3 ligases, according to whether they contain a RING, U-box or HECT domain. These domains are responsible for either directly catalysing the addition of ubiquitin or simply facilitating another E3 ligase to do so. RING and RING-like domains are by far the most common (<600). Exactly how these domains mediate the transmission of ubiquitin is not clear, but it can be via an E3-Ub intermediate or directly from E2 to the target. The domains are relatively standardised, due to the fact they bind to E2 proteins, which contain less diversity than target proteins. However, it's the combination of the E2 and substrate binding domains that generates the selection. 2
Target recognition
So how does the target come into all of this? Each E3 ligase recognises a specific sequence on the target protein due to it's own conformation and signal sequence creating a unique interface full of intermolecular interactions- just like any protein recognises any other protein. However, although individual cases vary, the tight control primarily comes from post translational modifications on the target. Phosphorylation in particular is common in signalling and may allow E3 to bind, inducing degradation of the target. I'll use some examples to demonstrate this point, but note that every case will be different.

c-Cbl (E3) recognises activated receptor tyrosine kinases and ZAP 70/Syk kinases (target) by binding a phosphotyrosine sequence through its tyrosine kinase binding domain (containing SH2 domain). The phosphorylation is controlled by other cellular signals
Glycosylation
Proline hydroxylation
Sumoylation

Other regulations of the process that are linked but perhaps outside the scope of your question include E3 post translational modifications (eg. autoubiquitination), sequestration of E3 via binding partners (Cand1 and Roc1), pseudosubstrates and substrate competition. 7
Misfolded protein degradation
Making protein is a large investment for the cell and so there are several protective measures to prevent misfolding/aggregation. Whilst there are many different types, chaperones generally work by isolating the misfolded protein and undergoing a series of binding release steps, triggered by hydrolysis of ATP. The protein can still be released unfolded, and the cell will continually try to isolate it for refolding. However, certain chaperones form a complex with the proteasome, and can recruit other UPS components. The choice to give up on refolding appears to be a stochastic process, and will depend on the concentration of the appropriate chaperones. Misfolded proteins tend to have significant regions of exposed hydrophobic residues, and E3 ligases are therefore likely to recognise this less specifically than the degradation pathway described above.
Relevant sources include endoplasmic reticulum associated degradation and chaperones.
Summary
The answer to your question is that there is no standard recognition sequence in E3 to know which protein to target, the binding needs to be diverse in order to give the control the cell needs. That means it could be anything, but each E3 is likely to be relatively specific for its target, and is often controlled by other post translation modifications on the substrate. Misfolded proteins can be recognised and degraded due to the association of the UPS with chaperones.
If you're really interested, you can download this file and open it in something like PyMol to actually see the ligase ready to transfer ubiquitin.

Ubiquitin is active as part of a complex of proteins. Other elements of the complex recognise the proteins to be degraded. These recognition or specificity proteins are responsible for targetting proteins for ubiquitination. They are called ubiquitin ligases.

That’s just begging the question. Now OP knows that ubiquitin doesn’t tag the proteins itself but they still don’t know how proteins are tagged, i.e. how E3 recognises the misfolded proteins.


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Any idea what this red plant is?
I live in South central Indiana, US, and these have just started appearing in the grass in my yard. I just bought this house last fall so I've never seen them. Anyone know what they are? Are they harmful to dogs?

It is indeed Mock strawberry and they are not toxic, from personal expirience and http://www.accessdata.fda.gov/scripts/plantox/detail.cfm?id=13794

We called those "Indian strawberries". They are also known as Mock Strawberry (Duchesnea indica). Survivalists are pretty familiar with this plant.

They are a lot like strawberries in appearance, but the berry is rounder, not pointed, and held upright (they point up) on the stem, not pending. Though the berries are edible, they don't have much flavor at all. The leaves are also similar, and the flower is yellow, not white. The fruit's seeds are the same color as the fruit. They flower late spring and throughout summer. Your specimen looks like it was nibbled on at some point. The inside of this berry is white and kind of spongy and dry (especially compared to the real thing, i.e. wild strawberries.) The stalk it's on is hairy (as it should be) but damaged, and only one part of the leaflet is visible in your photograph.

They're in the Rose family, but there's some discussion about what genus they really belong to; may be more similar to Potentilla.
See also http://www.sierrapotomac.org/W_Needham/IndianStrawberry_080617.htm


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What decides the position of the node of Ranvier?
The oligodendrocytes makes the myelin sheath in CNS and schwann cells make it in PNS. What decides where the oligodendrocyte or Schwann cell will attach and start forming myelin sheath? Is it genetically determined? Is it random? Is there any disease associated with improper positioning of node of Ranvier?

A combination of differentiation site, chemical guidance during migration, and signaling cues form a variety of sources.

The final step in the generation of an oligodendrocyte is the
  development of a mature myelinating phenotype, and this is largely
  regulated by axonal signals. It seems likely that both soluble and
  cell mediated signals from adjacent axons are integrated into the
  developmental profile of oligodendrocyte precursors resulting in cell
  differentiation, up-regulation of myelin gene expression and formation
  of the myelin organelle. Candidates for axonally derived soluble
  factors include FGFs (Bansal et al., 1996 and Qian et al., 1997) and
  thyroid hormone (Barres et al., 1994a and Barres et al., 1994b), while
  axonal cell surface molecules such as L1, MAG, NCAM and N-cadherin may
  regulate formation of the myelin sheath (Payne and Lemmon, 1993 and
  Trapp, 1990).

http://www.ncbi.nlm.nih.gov/pubmed/12385864
I don't know of any diseases that just mess with positioning but there are diseases that kill oligodendrocytes (like multiple sclerosis).

Thank you ! My question is actually not about how oligodendrocytes develop and migrate to neurons but rather about how , once they have reached their ,know where to form myelin sheath along the length of an axon.

Ah, ok, this is the same paper, but I have changed the quote to the more specific discussion of myelination;  short story: the axons themselves cue the oligodendrocytes.


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Subtypes of Acute myeloid leukemia
I am a computer scientist with no biological background and working on analyzing lab  results of patients with Acute myeloid leukemia. They have been tagged with following subtypes of AML:

AML with No maturation
AML with granulocytic differentiation
AML with monocytic  differentitaion.

I know there are two classifications for AML subtypes: FAB(M0-M7) and WHO. I think these patients have been classified using FAB, but their corresponding subtypes' names do not match in any of the names associated with M0-M7:  http://www.cancer.org/cancer/leukemia-acutemyeloidaml/detailedguide/leukemia-acute-myeloid-myelogenous-classified.
I checked a lot of literature but still not sure about the class of the last two tags in FAB classification. Could someone please help me with that?

"AML with No maturation"  is M1?
"AML with granulocytic differentiation" is M2 (or M4, M5) ?
"AML with monocytic  differentiation" is M4 or M5 or both ?


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Do we have enough diversity of antibodies to overcome almost any antigen?
I always wonder about the capability of diversity of our antibodies. Do we have enough antibodies to fit to every kind of molecule? Wont't it be easier if our antibodies are like clay and can be molded to any form by antigens? Why to waste energy producing so many types of antibodies?
If some pathogen makes its antigens just like antibodies of our body, (I think) they won't ever be detected. So what would our body do?

As my answer is quite big I've highlighted the different regions I answer your question.
Intro and basic info
I take it you know how antibodies are made, but as a quick recap they're made by VDJ recombination of a limited but still quite numerous pool of genes which are recombined randomly, and then further recombination occurs by hypermutation of certain segments particularly in the regions that identify antigens.
What is Hypermutation?
Hypermutation occurs after the original antibody is made in order to perfect it. The same mechanism I talk about in moulding antigens below. It is exactly what it says: a high rate of mutation compared to that of the low rate in cells normally. When B cells are activated because they've met their antigen to which they respond (cognate antigen), they undergo somatic hypermutation. While the B cells undergo somatic hypermutation, the genes which code for the antibody are mutated so that the antibody binds to its cognate antigen with a different specificity. If it binds better the B cell gets to live, if it doesn't bind or it is worse then the B cell dies.
Moulding antigens
What we cannot do is the other way around. We can't recognise an antigen and then make an antibody to it, because recognising the antigen requires an antibody. What we can do is once we've recognised the antigen, then mould the antibody so it is a better fit. How we do this is by B cells mutating their antibodies and competing which binds better. However, B cells just don't have the knowledge to see an antigen and think a tyrosine residue at this position will be perfect to change my shape to this configuration - that's really complex stuff!
Do antibodies recognise every molecule?
Antibodies are made to essentially every antigen which is very costly in terms of energy as you mentioned. In fact, the number of genes that make antibodies are thought to be the perfect amount as to protect us without being too numerous so that it is not only too costly, but we have so many different antibodies the chance of ever finding the right B cell is so low we die before we manage. This is because of the way antibodies are mass produced, in the typical pathway of new antigens, firstly a T cell must recognise the antigen then B cells that produce an antibody that binds to the antigen (rarely in the same region, and may not even be to a protein antigen).
So these two paragraphs highlight the limitations and answer your first question. Antibodies are so diverse that we can expect quite a few to recognise every pathogen, but not every single possible antigen will have a cognate antibody. Diversity without so much diversity that it becomes redundant. The second limitation is that antibodies will ideally not form if they recognise self (our own proteins etc.) Which leads on to your next question.
What if a pathogen makes antigens that look like our own proteins?
Autoantibodies are made but are typically non-pathogenic (i.e., they don't cause harm). Certain HLA/MHC polymorphisms that make us likely to form autoreactive T cells, also make us make autoreactive antibodies. Interestingly, this increases our risk of autoimmune diabetes but ALSO makes us more resistant to infection by HIV. This can be practically seen in the DQ8 polymorphism. This is a perfect example to illustrate the answer to your second question. Ideally, pathogens which have antigens similar to our own would not be detected. HIV wraps itself with an envelope of our own lipid membrane for this purpose, and the best neutralising antibodies are often self-reactive and therefore are those that failed elimination.
However even these pathogens are going to do something or make something that isn't something our cells usually do. This is how the body finds and targets cancer cells (in a way), they do things our own cells won't typically do like make the wrong proteins or wrong amounts etc. Thus cancer cells and pathogens can be targeted by our cells that find something that isn't self (CD8 cytotoxic/killer T cells). As for pathogens, we all make MHC/HLA which is unique to us and pathogens could never manage to invade and make the specific HLA/MHC that we do, so our body also targets missing HLA/MHC.

Wow !!! I really like your answer .....:)

Could you tell me what is hypermutation ?

Thank you! And yes, I've updated the answer to describe hypermutation briefly.

Loved your answer. But can you add a chapter about self tolerance and how CD8 cells recognize cells which produce wrong amounts of protein?

That's a question in it's own right @NeoDevlin, best imo to open a new question. It isn't as related to this question, if I come across it I shall answer it =]

I am not able to understand how mutating the gene for antibody and then giving the antibody a new specificity could be accomplished. Is this mutation random , if so, there cud be many combos which were harmful and most of the cells wud die.   Please help.

Yes, it is random and most die. But that's normal, some studies say up to 99% of B cells die. It just shows how important the immune system is that it is actually advantageous to be that wasteful.

The structure of a protein is largely dependent on what it is supposed to do. There is a little bit of wiggle room, but essentially, major changes in structure will also change the function of the protein.
This is why it would be difficult (though not entirely impossible) for a pathogen to successfully change all its surface antigens into close-enough mimics of the host antigens that the host immune response is completely evaded. Antibody CDRs are extremely sensitive, and a change in even a single amino acid of the epitope is often sufficient to trigger a full-blown immune response.
In addition, antibodies are only one of the many mechanisms (albeit a very important one) by which the immune system detects and eliminates invading pathogens, so even in the case of failure of the antibody system, T-cells and the innate immune system should generally be sufficient to initiate an immune response.


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Plasma cells and memory cells
What decides whether an activated B cell will get converted to plasma cell or memory B cell? Is it necessary that out of a mitotic division one will convert to memory B cell and the other to plasma cell?

A summary of what we know so far includes that for B cells to become plasma cells they need BLIMP-1. For memory cells CD40 engaging with CD40L on B cells is required. CD40 is expressed on Th cells and thus they are also necessary for memory cell development. Problem is though, it's really damn confusing after that. It really isn't known but if you're interested in this stuff consider reading this review which talks about memory cell differentiation and this which discusses plasma cell differentiation.
The image below helps (taken from this review)
PC = Plasma Cell, MBC = Memory B cell


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What stops the coagulation process?
Whenever there are minor/major injury to blood vessels, the platelets, fibrin, thrombin, etc. are recruited. They then seal the wound and block bleeding.
What tells them that their job is done?

This paper seems relevant: Dahlbäck. 2005. Blood coagulation and its regulation by anticoagulant pathways: genetic pathogenesis of bleeding and thrombotic diseases.

Exposed collagen at the site of vessel damage simultaneously initiates plates aggregation and the clotting cascade. So, when the wound is sealed and no more collagen is exposed, which is the main factor to activate the cascade, the blood clothing cascade stops.


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Male behaviour during breeding season
The mountain blue bird build nests to attract females and exhibit aggression towards other males during breeding season. Which of the following is likely to give the birds maximal evolutionary fitness?
a) stronger aggressive behaviour only during egg laying
b) stronger aggressive behaviour during nest building rather than during hatching of eggs
c) stronger aggression when egg is first laid than during nest building
d) greater aggression during hatching eggs than during nest building

Can you provide some of your thoughts on what the answer should be (and why?)? I personally think it is too less information to decide upon, but taking a thought-out guess, I think it can be (b).

@SatwikPasani Yes the answer is b. What did you think ? I am really confused with the question.

For the trait to be beneficial it needs to happen before mating. If the male scares off other males but the bird has already mated with another bird it wont be beneficial. So the answer is B, because its the only answer that happens before mating

a) stronger aggressive behaviour only during egg laying
c) stronger aggression when egg is first laid than during nest building
d) greater aggression during hatching eggs than during nest building

These all occur after the stage which determines fitness. Egg laying (a and c) and Egg hatching (d) occur after the male has won the right to mate.

b) stronger aggressive behaviour during nest building rather than
during hatching of eggs

Assuming the behavior increases mating success and fitness, the answer is B because this is the only strategy that attracts more females and gets rid of rival males before it is too late (i.e. before the female mates). This is also assuming that the female can/will only mate once.
In chronological order the answers run "B,C/A,D" (C & A are really one and the same in my eyes). Mating occurs between B and C.


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How does a biologist decide when she has enough results to publish a paper?
Biology is so exciting! Answering a question leads to  thousand more questions! There is no limit to how much one kind find out about a phenomena…
So I have always wondered how someone can decide that it is time to publish some fixed amount of research they have done. How do biologists decide when to publish a paper? How do biologists know that results are sufficient enough for a publication?

haha... when reviewer is satisfied :P

@WYSIWYG And I believe there are  money constraints too!

not much.. just advertising constraints

@WYSIWYG By money, I mean funding ... What exactly is advertising ?

Reviewers/referees are indeed the gatekeepers and they hold the key and they can make it quite difficult to publish a good work! Money is most certainly a constraint for the scientists that have to pay for the paper especially to make it open-access although many funding bodies these days pay for the publication costs! The journals however take advantage and they charge astronomical amounts for advertising and only allow the highest bidder to advertise as they self impose a space limit, hence they become choosy over it, which becomes a constraint on their part.

I agree with all the responses so far; however I thought I should add that to publish a paper in a decent internationally peer-reviwed journal, more often than not, a paper has to tell a story, ideally a novel story and not just the same data that has been published before or at least address an old question in a new manner, that provides a fresh insight into the field or the question. A publication can't just be a bunch of random small and unrelated questions and experiments, at least not in any peer-reviewed journal. The key to a successful paper is that it should have ideally one message, which can be identified in the title, since believe it or not thats how most scientists vet whether a paper (abstract/summary) worth looking at or not. So as correctly mentioned, you identify a gap in the knowledge and attempt to address it having considered what is know about it so far, if any. Writing a paper follows a global formula, which has been elaborated in Chris response. Hence the key is that the paper has to tell ideally one story and the experiments used to address it has to make a logical progression to address the question. So you can't just jump from a small preliminary experiment which is questionable in its reliability into a large scale experiment. Some times you have to make the leap of "faith" in your experimentations and just do a certain experiment but the chances are your previous experiments have given you an indication as to whether its going to work or not. Be very mindful that most of the time the order in which you do your experiments is not the order in which you put them in the paper so what usually happens is that you have a central question, you do a bunch of experiments to address it and then you shuffle them around to tell the story in the most concise way and again the key word here is story.
Now not only a paper has to tell a concise story but it has to be of general interest to the scientific community, specially in high impact journals. You probably know a recent paper about STAP cell lines that got into Nature and attracted world-wide attention in which the authors described how exposing the cells to stimulus/stressors such as acid or pressure can turn it pluripotent, which the media linked to personalised treatments. Now I don't want to get into all the controversy that followed it but its just to make the point that a research like this is not only of interest to the scientific community but also the public hence it got published in a highly respectable journal. Now whether thats the right thing for scientists to do and send important research to the top journals, which is hard to access by many countries is a whole different argument but I hope you can begin to see publishing a paper in a journal is not only related to its scientific merits but also to what extent it is of interest to the general or scientific community and what story is it telling or implying (to put it a bit more crudely). Now not every paper makes it to Nature and most of the time publications are highly specialised work which not everyone on the planet might be interested in them but they still follow the points I talked about.
hope this helps!

When you do science you start with a question or a hypothesis. How is Gene A regulated? Or "does hormone B have an effect on the immune system". Or whatever.
Then you start by thinking how you can prove or disprove your question/hypothesis with experiments. You then do your experiments and see if they are enough to prove your question. It often happens that you have to do additional experiments to cover side-questions which appear during the work or to exclude some side-effects which may also be important. If you have done all this (with replicates) and looked from different angles on your problem, then you can start writing an article.
This includes some introduction from the literature and a classification of your results into the things already known. If you make strong claims, then you will need a lot of arguments (=results) to prove your point. It is quite hard to argue against "common knowledge".
The question of how much research is enough is quite philosophical, since you usually don't "finish" a topic. You look only at certain aspects from a certain angle. This can be quite different for other researchers.

"..since you usually don't "finish" a topic".. I just love this line !

It is really like this. Working on one question often throws up two or three new related questions. That's what makes science to exciting. Of course you need quite some tolerance to frustration, as not everything works as intended or as it should.

It's all about "Is this paper interesting enough to get published?"  And people just get a feel for that when they are reading papers all the time, and submitting papers frequently.  For instance, maybe publicizing a big cool dataset was useful enough a few years ago to be published as is, but now, you might need a good finding that you found from that dataset, and followed up on, before the paper will be considered by your journal of choice.

Thats right. Standards change and people get used to some findings if it is shown the 10th time.


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Why is Turner syndrome rarer than Klinefelter syndrome?
Turner syndrome occurs in 1-1000 to 1-5000 females, and Klinefelter syndrome occurs in 1-500 to 1-1000 males.
Why is Turner so rare even though they both are caused basically by the same mechanism?

First of all, they are not caused by the same mechanism. They are both aneuploidies, but the mechanism is different.
Turner syndrome happens when one of the gametes (most commonly father's) lacks a copy of X chromosome, or the X chromosome is heavily damaged. This means that while normal women have two X chromosomes, Turner women have only one, and nothing else.
Klinefelter syndrome happens when one of the gametes retains an extra copy of the X chromosome. This way a Klinefelter man has two X chromosomes and Y chromosome instead of one X and one Y.
As you can see - the Turner woman is lacking some genetic information, while the Klinefelter man has too much of it. Generally, having too much genetic information is much easier to survive than not having enough of it, so this explains the relative difference on the most basic level.
But, you might say, what about Barr's bodies? Don't the women use only one X chromosome in each cell? And wasn't Y chromosome almost empty?
Yes, these are an important consideration for these two syndromes. In each cell of a women's body one of the X chromosomes is inactivated and folded into a Barr's body. This inactivation is random, so part of the cells keep mother's and part of the cells keep father's X chromosome active. The trick is that the Barr body is not entirely inactive (Genes That Escape From X Inactivation). Only about 15% of the genes are active, but just the lack of them is mostly lethal (Turner fetuses are usually aborted, Wikipedia quotes olny 1% surviving until birth), and accounts for the health problems and deformations in Turner women.
A Klinefelter man has two X chromosomes in addition to his Y chromosome, so one of the chromosomes inactivates into a Barr body. The presence of Y chromosome directs his body to develop into a male pattern, but at the same time, the existence of Barr's body with those still active genes, causes his body to develop also feminine features. There is little to cause spontaneous abortion.


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How HIV Affects and Its Treatment using Combination Therapy
Can someone please help me with the following questions. I've written my specific questions right after the text question.

Human immunodeficiency virus (HIV) is a retrovirus. Its genome is a single (+) stranded RNA that is packaged with the reverse transcriptase enzyme within a protein capsid. This is further packaged into an envelope that is derived from the plasma membrane of the host cell in which the virus had replicated. The surface of the envelope is covered with the envelope glycoprotein, called gp120 & gp41.
a) HIV specifically infects the T-helper (TH) cells of the human immune system. If the HIV enters the host cell by means of host receptor recognizing a viral protein, what would be the most likely ligand and its corresponding receptor during HIV infection?
b) Some individuals are resistant to HIV infection even after repeated exposure. Assuming that these individuals express a normal level of the functional receptor that you have recognized above, how can you explain their resistance to HIV?
c) In recent years, therapies have been developed to fight AIDS using nucleotide analogs. The drug used to combat AIDS is Azidothymine (AZT). The structure of AZT is very similar to thymidine except that in AZT, the 3’-OH group on the deoxyribose sugar is replaced by an azido (N3) group. Which process of the life cycle of HIV do you think is inhibited by AZT?
d) Combination therapy is the new treatment strategy for treating HIV patients.
i. Why is combination therapy more successful in preventing the emergence of the disease resistant clones?
ii. If the combination therapy involves a drug that prevents…
1) HIV binding to the target cell, what protein does this target?
2) Integration of HIV genome into host cell genome, what protein does this target?
3) The cleaving of viral polypeptide into individual proteins, what protein does this target?
e) If the AIDS patient were given combination therapy, would the patient still be able to transmit the HIV virus to his/ her partner (Yes/ No)? Explain your choice.
**
a) No idea.
b) Maybe their T-helper cells have some sort of mutation that makes it impossible for HIV to bind to them?
c) I'm thinking "formation of HIV RNA" because in the absence of 3' -OH bonds, phosphodiester bonds cannot form.
d)
    i. It kind of makes sense because a virus being resistant to multiple drugs would be very unlikely but maybe there's some definite reason why?
ii. No clue. Is this talking about proteins of the virus or of the host? Also, enzymes are also proteins, right?

Is this a homework question? If so, use the tag.

a) HIV uses a certain receptor that's expressed widely on T helper cells. As this is homework I suggest looking at the wikipedia article to look this up for yourself. It is under tropism.
b) You mentioned mutation. That's very true but this question is excluding people with that mutation called the delta 32 mutation. Thus HIV can infect these people, but what happens to any virus in the context of infection? How does the human body deal with viral infections. Is there any variation that would account for why some people can be resistant to HIV and others not be?
c) Yes! Well done :) You're thinking along the right lines. Look up the drug on wikipedia and look up it's mechanism.
d) i) Yeah exactly that. But more than that. There's optimal HIV which in the absence of drugs does the best job at infecting. If we give a drug then HIV has to mutate away from optimal HIV to stay alive, but it's weaker. Give multiple drugs and it can't mutate away from all of them because if it did it would be so far from optimal it would be a rubbish virus.
ii) 1) It could affect the HIV binding receptor protein or the protein with which it binds on the host cell. So both! Logic would dictate we would use self receptor blockade because at least they're more conserved but I'm sure both are probably used. Enzymes and receptors are both proteins.
2 + 3) Look up the lifecycle of HIV
e) Theoretically possible. He might not take the drugs. If he takes the drugs unlikely because the virus basically becomes undetectable. Look this up, it should be on wikipedia again.


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How can a continuous RNA be transcribed in the lac operon?
The lac operon has 3 genes: lacZ , lacY and lacA. I have seen that the m-RNA transcript of these genes has stop codons in between. So, how can the RNA be made continuously? Won't the RNA Pol detach if there is a stop codon in between?

RNA Pol doesn't worry about stop codons.  Transcription termination can occur through the formation of a hairpin in the new RNA sequence, or through the action of Rho proteins.  A lot of the time prokaryotes have polycistronic mRNAs, that is, mRNAs with multiple protein coding regions.  The stop codons are detected during translation, so you will often have all three lac proteins being translated at once off of the same mRNA.
Here's a nice section on transcription termination, or look up Rho-independent or Rho-dependent transcription termination for more info.

... and then there are three separate Ribosome binding sites that may act to attract separate ribosomes to create the distinct proteins from a single mRNA copy of the gene...


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What is the advantage of restriction enzymes cutting only at specific sites?
Bacteriophages have sequences which often do not have specific sites for restriction enzymes of bacteria to cut at and so can attack the bacteria.
Wouldn't it be better if bacteria had something "universal" like an enzyme that simply cuts the nucleotide sequence "randomly"? Is there any particular advantage of cutting at only a few restriction sites?

Such universal restriction enzymes would be very dangerous to leave lying around even if contained within a vacuole. Remember that bacteria are prokaryotes and have no nuclear membrane to protect their DNA.
The analogy would be having a burglar alarm capable of burning down the house in order to protect it against thieves.

But bacteria can definitely protect against it by methylating their own DNA or by any other mechanism.

You mean methylate the entirety of their genome?

You are right , it would be really difficult . Thanks !

Methyltransferase is just an enzyme.  The cost of failure seems high if a reversible reaction must protect each and every codon.

Yes ..In case of restriction sites , they would have to methylate just those areas.

So can I say this is a compromise between protecting the bacteria from any bacteriophage and the cost of continuously maintaining a methylated genome ?

Sometimes the best defense is a good offense.

Notice that viral DNA is not the only foreign DNA that a bacterial can meet during its bacterial adventures. Plasmids, conjugated DNA and DNA inserted by transformation exist, and it may confer ecological advantages. Because of that, even if the enzymes would recognize only non genomic DNA and destroy it effectively, it's still more useful to have some criteria and allow to stay some alien DNA, while destroying some other.
Restriction sites are pretty small, so the chances of getting one target in a viral genome is quite big. Bacterial DNA is protected by methylation, which is recognized by this enzymes and prevents them to break the DNA.
Restriction enzymes are not the only means bacteria have in order to defend from foreign DNA. Bacteria usually carry exonucleases that recognize single stranded DNA and linear DNA, which is common in viral genomes, but not in non-infected bacterial cells. This enzyme lacks the specificity that restriction systems possess, and can work combined (for instance, a restriction cleavage may form linear DNA, which will be detected by exonucleases as potentially harmful DNA).
In addition to this, bacteria and archaeons have a special antiviral defense, named CRISPR-CAS system, that acts like an immune system. CRISPR-CAS inserts in a special region of the bacterial genome viral DNA fragments from previous infection. When a new virus infects the cell, those viral fragments are expressed as a special kind of RNA (CRISPR-RNA) which, if the virus has already infected this cell, will attach to viral DNA and will serve as a marker. Then, the RNA-marked DNA is recognized by special nucleases. This defense system allows to obtain acquired resistance that (unlike vertebrate immune system) is also inheritable.
Concluding, not all foreign DNA is harmful, since plasmids and other could provide some advantage to the cell. Restriction-modification systems aren't the only defense system that the bacteria has against foreign DNA, but all of them must be able to differentiate between desirable and harmful DNA. The combination of many different defense systems allow to patch the limitations of them individually, and so different species will invest differently in one or other, depending of the ecological pressures they have to face.

Restriction enzymes are only half of the system. The other half is the methylation system. The majority of restriction enzymes won't cut at their target site if it is methylated in the correct way. The system works to identify foreign DNA because the foreign DNA is not methylated in the correct way so it will be cut but the bacteria's own DNA is methylated so it will not be cut. Think of it as a lock and key mechanism.
A generic DNAase wouldn't be able to function in this fashion.

There are generic DNA cutting enzymes! E.g. DNase A  (journal), DNase I  (wikipedia), and NucA (Bacillus subtilis annotation). The outer layers of human skin contain active dnase, with just such a protective role as one apparent reason. This is one of the (many) sources of contamination that can mess up dna experiments.


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human immune system

The common cold and [some?] types of influenza are self-limiting.
Some microorganisms cause self-limiting diarrhea.
Is tuberculosis [potentially] self-limiting or not?
To put it another way, suppose that ONLY ONE viable cell of
Mycobacterium tuberculosis enters the respiratory system of a
healthy human. Will the immune system of that healthy human be
able to defeat, on its own, that lone Mycobacterium invading cell?
Is the human immune system capable of defeating M. tuberculosis?
If the answer to question number 1 is yes, then my follow up question
is this: Is the human immune system capable of defeating, on its own,
all other pathogenic microorganisms (bacteria)? How about pathogenic
viruses (except HIV)?
As a non-medical professional (although I am a medical enthusiast), I
notice that self-limiting viral diseases are more common (both by
type and prevalence) than self-limiting bacterial diseases. Is this
observation correct?

Edit:
To clarify: Yes Chris, for "self-limiting", i mean an infection that resolves by itself without an external intervention (no antibiotics, antivirals, vaccines, etc.).
I am interested in the [theoretical] capabilities of the [unaided] human immune system. I live in a third world country where pulmonary TB is prevalent. Most of the self-limiting diseases i know are viral, and at this moment, i cannot name a bacterial infection that resolves without antibiotics. Nevertheless, i can't help but wonder why we humans can handle viral infections, but [apparently] not bacterial infections. And this got me asking long ago: is the human immune system incapable of defeating M. tuberculosis? Aside from bacteria that cause diarrhea, what are other examples of bacterial infections which the human immune system can clear on its own? What about fungal infections?

Do you mean by "self-limiting" the fact that an infection comes to an end without an external intervention?

To put it another way, suppose that ONLY ONE viable cell of
  Mycobacterium tuberculosis enters the respiratory system of a healthy
  human. Will the immune system of that healthy human be able to defeat,
  on its own, that lone Mycobacterium invading cell? Is the human immune
  system capable of defeating M. tuberculosis?

Yes, for example by vaccination you prepare the immune system for recognizing M. tuberculosis. After that it will have a greater chance to defeat the infection. Without vaccination it depends on the genetics, the immune system and the health state of the individual. E.g. starving people are more vulnerable to TBC.
The minimum infectious dose of M. tuberculosis is very low, so it is possible that a single organism can cause infection. Be aware that the infectious dose depends on the type of the disease. So by other diseases your immune system can defeat a large amount of invaders and you don't even recognize it, because you don't get sick.

If the answer to question number 1 is yes, then my follow up question
  is this: Is the human immune system capable of defeating, on its own,
  all other pathogenic microorganisms (bacteria)? How about pathogenic
  viruses (except HIV)?

It depends on the individual. As far as I know for a certain disease some percent of the population is always resistant. Even by HIV about 1% of the population is resistant. I think it is even possible that somebody defeat HIV without special genetic resistance, however this happens rarely, because the minimum infectious dose is very low by HIV too.

As a non-medical professional (although I am a medical enthusiast), I
  notice that self-limiting viral diseases are more common (both by type
  and prevalence) than self-limiting bacterial diseases. Is this
  observation correct?

I guess you mean that diseases with low fatality rate are more common. In western countries this is true, because the healthcare system prevents epidemics of lethal diseases with quarantines. In less fortunate countries I am not so sure about this...


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Why do bats huddle during late fall?
In the late fall, bats hibernate in clusters with many bats pressed together and holding on to one another. Which of the following supposed advantages of huddling behavior is, in reality, not true?

Any heat generated by any bat is shared by other bats.
Less surface area is exposed to the environment.
Huddling behavior decreases the amount of food needed for bats to stay warm.
In this configuration, less heat is needed for each bat and, therefore, each bat requires less food.
Huddling behavior helps bats stay warm while they feed.

this looks like a homework question!  we don't play that here.

@shigeta she did actually tag it as homework.

Think about where/when bats huddle, where/how/when they feed.

@biogirl What do you think? What's your reasoning so far?

ok fair enough.  still this seems like a hard one to help with.  'one of these things is not like the other' is about all i would say.

@kmm I think huddling helps them stay warm but the answer given in book is 5th. I think 3rd and 4th say the same thing and 1st and 2nd are definitely true.So only 5th can be the answer but I think huddling behavior does help in staying warm .

Huddling behaviour can help in staying warm, but think about @terdons comment some more.

This is basically a trick question and a bit of a cheap shot. All of the reasons cited boil down to "bats huddle to conserve heat", they are basically the same, single, reason.
In order for bats to feed, they need to move, fly out of their cave or wherever they happen to sleep and go forth and look for food. Therefore, they will not be able to huddle while feeding because they will be flying around trying to find fruit or donkeys or whatever each species feeds on. Unless they can figure out a way to huddle while flying, they will not be able to huddle while feeding and so number 5 is wrong.


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What is possibly wrong in my gel electrophoresis when I didn't see bands of DNA ladder on gel?
What was possibly wrong in my gel electrophoresis when I didn't see bands of DNA ladder, and genomic DNA sample on gel ? I could see bands of genomic PCR and RNA solution.
Edit
Thank you all of guys for sharing your opinions. From some opinions, I found out the possible error that my genomic DNA didn't show up because it was not pure (I forgot the detail that our group used a sample of DNA which was extracted from a previous lab and we didn't obtain an expected ratio for the purity of DNA. Then, we also used the impure DNA sample to do PCR, and finally used the amplified DNA for gel electrophoresis lab). However, the reason for DNA ladder didn't show up I'm not sure. I just can suppose that my groupmate who handled with DNA ladder solution possibly contaminated it.

Can you tell us how you are visualizing the gel? The answer probably revolves around the way the gel and samples are prepped and imaged.

Perhaps your ladder has gone off!

Can you show an image?

I observed it under a UV-spectrophotometer. Actually, the bands which I observed was RNA/cDNA RT-PCR product, genomic PCR product, and RNA solution, but the bands of genomic DNA sample and DNA ladder didn't show up. I set the voltage to 120 and allow to run for 30 mins which worked for my classmate.

This picture is still not very clear. Don't you have a gel-doc in your lab?

I know the image is not good. My groupmate took it.

So that isn't your ladder on the far left side of the gel?  How about some lane labels.

No, it's just a ruler on the frame of the mold. Acctually, I don't have any bands of DNA ladder and my teacher also suppose so.

This question appears to be off-topic because it does not provide sufficient details required for a precise answer. Questions related to experiment troubleshooting should provide all necessary details about the experiment.

I'm not talking about the ruler.  I'm talking about what's fluorescing pink down on lane 1, starting from the left.  That looks like poorly resolved and partially degraded ladder to me.  What was your gel composition?

Just to help you with future gels, take the gel out of the plastic and put it right on the glass. The plastic can absorb some of the UV and reduce the intensity in your dye, which I'm assuming is ethidium because it's pink. Also, are you using lithium borate buffer with orange G loading buffer? The voltage and time you mention are consistent with that, and your dye front is yellow, but you have a second dark blue dye front near the top. But we shouldn't have to guess at your experimental details.

Possibly You don't mix ladder containing microtube by Sampler. You should slowly Fill and emptying Sampler for several times when pick it for use, mix it well, but do it without creating a bubble.one more thing, check your ladder by "NanoDrop"

Do you think a sample of DNA which was not pure can influence to my result? Could you explain more why creating a bubble can cause a bad result, please?

@Kim well, there are number of reason in each part of protocols lead to make bad results so each idea that friends have mentioned are also considerable and having Inappropriate sample is one of them. creating a bubble can cause a bad result because When you use small amount of Ladder so if bubble will be taken as samples, your measurements will be very low and inefficient. I propose check process of preparation of Ladder work.

@Kim can you please check your ladder by nanodrup?and compare result for each of DNA and RNA and proteins?

I'm afraid I can't. You know, we just could follow a protocol which was given to us. I was doing the experiment for a class at college level. What is nanodrup?

@Kim For more information about nanodrup please visit this and this links


text:
Inheritance of Huntington's disease
People with Huntington's disease have HTT genes with more than 37 copies of CAG repeat. The risk of extra copies being generated is higher during sperm formation than during ovum formation. Why is it so?
Interesting fact: People with HD allele inherited from father develop symptoms earlier than if that allele is inherited from mother.

Excellent question. The answer is that, in general, there is a higher rate of mutation in spermatogenesis compared to oogenesis. This is because there are more cell divisions during spermatogenesis, which allows for opportunities for mutation.
In addition, repeat diseases like Huntington’s sometimes have a phenomenon known as anticipation. This is when the disease gets phenotypically (and genetically) more severe with each successive generation. The exact molecular basis of this is not completely understood, but it is just well known that DNA polymerase tends to make more mistakes in large repeat regions, causing an expansion of the repeat. Anticipation is not linked to gender, I just wanted to point out that these repeats are prone to mutations that will expand the repeat and cause disease
You can see anticipation in this graph. This example is for Fragile X. The higher the repeat number in the parent, the greater the chance the child develops the disease. The parent doesnt have the disease, but what happens is the repeat mutates and gets expanded to the point where the disease will develop.

So, put these two facts together and you have your answer. A male's sperm tends to have a higher overall mutation rate, and the region responsible for Huntingtons is already prone to disease causing mutations as it is. The result ends up being the disease gets ‘inherited’ more often from the father
Picture from here

Awesome answer ! Could you tell me what is the difference between total CGG repeat length and pure CGG repeat length ?

In fragile X the repeat is CGG. But sometimes there are also AGG repeats as well. Pure counts only the CGG repeats, while total includes both. This paper was trying to find the importance of AGG repeats on the disease

If they were trying to find the importance of AGG repeats, then why did they count pure CGG repeats ?


text:
How is antibody production stopped?
Once clonal selection is done, B cells would start dividing and producing antibodies. So, after an antigen is eliminated, what stops the division of B cells and antibody production?

Upon activation plasma B cells upregulate death receptors as part of being activated. Presence of the antigen overcomes the death signal, thus the cell survives. When antigen is lost, the death signals overcome the survival signals as there is no antigen, so the B cell dies via apoptosis.
Memory B cells don't do this. They survive and continue to produce antibodies for years, although this slowly wanes. Antibodies have to be produced as antibody mediated immune mechanisms are extremely important for memory and the reason why a subsequent infection is cleared so rapidly. Furthermore for the example of HPV, antibodies induced by the vaccine prevent the virus even infecting cells (so called neutralising antibodies).

You are right to say that Plasma Cells are terminally differentiated, so they don't become the memory cells, or calm back down or anything. But all Plasma Cells are not the same, there are Short-Lived Plasma Cells (SLPCs) that are less specific, but arise rapidly after stimulation, and there are Long-Lived Plasma Cells (LLPCs) that come about later and have more specific antigen binding.
SLPCs are rapidly activated, but also rapidly lost. These are the cells that Android was talking about when s/he said that apoptotic programs are initiated as soon as cells become activated and are eventually eliminated by these mechanisms.
LLPCs are the cells that stay in your body for a much longer time (theoretically for life, but probably not practically unless you get hit by a bus in a couple of years). When you get a vaccination, these are the cells that produce antibody that can be detected in the blood for a number of years (what testing your antibody titer looks for). These cells are in pretty limited supply, so we know less about them. My guess is that they are not actively eliminated, but may become eliminated over time by other mechanisms (purposely undefined here).

My understanding of this question is: Antibodies are produced by plasma cells which are terminally-differentiated B cells. Maturation of B cells to plasma cells is stimulated by the presence of antigen (T cells, cytokines, etc. etc).
In the absence of antigen the existing plasma cells undergo apoptosis, and the maturation of the cognate B cells will not be stimulated, so no more plasma cells will be produced.
I have found it surprisingly difficult to find references in support of these statements, although there is a large literature on the suppression of apoptosis in memory B cells.

Alan, you might try Ralph Zinkernagel's review: http://www.ncbi.nlm.nih.gov/pubmed/24909054. I don't have full access to the article, but it appears that he summarizes work showing the half-life of various types of Plasma Cells. I'm not sure to what extent anyone has looked into the apoptosis pathway that may be involved in these cells particularly.  Klaus Rajewsky has done work assessing the half-life of naive B Cells. It's possible that he has a review somewhere that can point you in the right direction. Good luck - and please post anything useful you find here.


text:
Why are low throughput methods more trustable for protein interaction?
I read that protein interactions found using high throughput methods are less trustable than those found using low throughput methods.
For example, searching for interaction of BRCA2 on BioGRID, I got this result.
So, we won't be sure about the interaction of BRCA2 with SIRT1 as it has been found with a high throughput method.
My question: Could you give me a very simple explanation of what is the meaning of high and low throughput techniques ? (I have a vague idea reading it on web but I am not satisfied with my understanding.) Why is high throughput not reliable in this case?
One reason I can think is that they involve mostly in vitro studies.

This article is a bad example, it has been retracted. See here.
But this doesn't matter for the methods.
This is usually done by so called "genome wide association studies". There you compare the regulation of your group of interest with a "normal" group to find genes which are differently expressed. This is something we did: We overexpressed a transcription factor in a cell line and compared it to the untransfected cell line, which doesn't have this factor. The comparision brings up differently expressed genes. This is either done with microarrays or today more like by ChIP-sequencing (let me know, if you want to know more, I can go into the details).
When you analyze such data, you first cut-off all data, which is below a certain threshold to be sure, that you reduce the number of false positives. A low threshold for the recognition of changes means that you are more likely to have false positive genes in your final list. This might happen due to changes in the cell or the conditions, secondary effects and so on. And you will also have signals, which appear statistically and which are false positive.
If you choose your threshold too high, you will reduce the number of false positives, but on the downside you will also generate false negatives, since you refuse genes which only have a relatively low change but are real. The balance between this is not always easy. As a rule of thumb usually everything which changes at least twofold in expression is used (unless you control better).
Even when filtered, the output of the experiment will still contain some false positives. Then you will also record some secondary effects, meaning that you gene of interest regulates a second, which regulates a third. Since both will come up in the analysis, it will look like that the third gene is regulated by the first (and not the second, as it would be correct). And these are the reasons why usually every intereaction between two genes (or better: Between a protein and a gene when talking about a transcription factor or two proteins) needs to be verified in the wet lab. And this is work, which can be pretty hard.


text:
How do plasmids protect themselves against restriction enzymes?
How do plasmids protect themselves from restriction enzymes released by bacteria (i.e., against bacteriophages)?

The strains that we use in the lab have defective restriction machinery.
In the case of DH5α it is mostly because of the endA1 and hsdR17 mutation. The former mutation eliminates an endonuclease that can degrade plasmids and the latter one eliminates the restriction system.
Check this.

What about the plasmids naturally present in bacteria ?

usually they are compatible and have undergone methylation at these restriction sites. since you compared it with immune response i'll give you an analogy. The proteins that are already present in the system are not considered antigens because the immune system actively tries to not launch a response against them. Similarly the natural plasmids are marked to be treated as endogenous. You may ask how they acquired the plasmids in the first place which is something like a chicken-egg question; the likely explanation is that they acquired it during the time of stress (nutrient deprivation etc)


text:
Carbon sink and carbon storage
Articles commonly state examples of carbon sinks are plants, soils, and oceans (e.g., link). My understanding is that carbon sinks must directly take up carbon from the atmosphere. Therefore, other organisms such as herbivores and carnivores are not considered carbon sinks (I understand their roles as carbon sources) although they store much carbon. Is this interpretation true?
If so, what is the main mechanism that soils (independent of plants) directly absorb carbon from the atmosphere? It looks as if most articles simply say that soils contain much carbon from plant organic matters, which is a carbon store rather than a carbon sink.

According to Wikipedia:

A carbon sink is a natural or artificial reservoir that accumulates and stores some carbon-containing chemical compound for an indefinite period.

The key point here is the "indefinite period" part. For example, although my body stores some kg of carbon, I can't qualify as a carbon sink because most of it is likely to be released again in some decades.
On the other hand, soils store large amounts of carbon, and as the soils keep developing that amount tends to grow, making them an effective carbon sink. The mechanism consists mostly on accumulating organic matter, as you say, but as long the amount of that organic matter keeps growing, soil works as a carbon sink.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Why are $\beta_2$ receptors present on bronchial smooth muscles , considering that they have only parasympathetic innervation?
It is well known that the bronchial muscles have only parasympathetic innervation. But they still express $\beta_2$ receptors. How does this system still cause bronchial relaxation? What is the exact mechanism?

Do you have a source for the first statement? I find that the first sentence here: https://www.ncbi.nlm.nih.gov/pubmed/11240156 seems to contradict it. Halfway through the abstract might be the answer to your question.

To be frank... I really just referred a single source .... The source is Rang&Dale's Pharmacology Ed-7 Chapter 12( Chemical mediators and the Autonomic nervous system) Pg 141. The exact statement is " Bronchial smooth muscle has only a parasympathetic (constrictor) innervation......."

The exact statement is " Bronchial smooth muscle has only a parasympathetic (constrictor) innervation (although its tone is highly sensitive
to circulating adrenaline—acting probably to inhibit
the constrictor innervation rather than on the smooth
muscle directly)."This gave the impression that there is absolutely no sympathetic innervation , when the case is the contrary! Thanks for directing me to the above paper!

Good question, but first I'll address a note in the comments.
In bronchial smooth muscle, do β2 receptors receive sympathetic innervation?
Canning and Fischer (2001) claim that bronchial smooth muscle do receive sympathetic innervation. But it would still be correct to say that β2 expression plays little role in regulating smooth muscle tone in the human airway under normal conditions.
How do β2 receptors cause bronchial smooth muscle relaxation?
You already know that this receptor is associated with bronchial relaxation. An article by Billington and Penn (2003) claims it works through Gs coupling. This binds adenylyl cyclase causing it to form cyclic AMP which activates protein kinase A (PKA) which carries out many more functions.
WHY are β2 receptors present on bronchial smooth muscles considering [minimal sympathetic] innervation?
Circulating chatecholamines released due to emotion, exercise and the like. Billington and Penn (2003) note "prophylactic bronchoprotection" as the central role for Gs-coupled receptors in airway smooth muscle.
Why ELSE are β2 receptors present on bronchial smooth muscle?
β2 receptors are important in regulation of airway smooth muscle cytokine/chemokine synthesis, and inhibition of airway smooth muscle growth (DNA synthesis/cell proliferation) i.a. (Billington and Penn 2003).

Billington, CK, Penn, RB 2003, 'Signaling and regulation of G protein-coupled receptors in airway smooth muscle', Respiratory Research, vol. 4, no. 1, PMID: 12648290. https://www.ncbi.nlm.nih.gov/pubmed/12648290

Thanks a ton for the clear explaination! It is a massive help!


text:
What's the relationship between snail movement and rain?
I have a question about the relationship between snail and rain. A few days ago I found snail shells in a moist area and I brought them in for crafts work (I thought they were empty because snail usually come out if you poke them). After a few days it rained, and I found that the snails have moved from the space i put them in (but not far). My question is why did they move after it rained  outside but not when I brought them in a week before?

The movement of organisms towards water is termed hydrotaxis. 'Hydro-' refers to water and '-taxis' refers to movement. Hydrotaxis has been investigated in animals such as the nematode Caenorhabditis
elegans (Wang et al., 2016) and, closer to snails, the gastropod Littorina
littorea (Gendron, 1977). Animals may sense the water content of their surrounding environment and moisture content in the air to move where they are more comfortable.
Animals need specific amounts water in their bodies to allow effective metabolism. We can control our bodily water content by taking a drink but simpler animals aren't afforded that luxury so they need to move towards/away from water. Your snails likely moved because the water levels in their bodies dropped as they 'dried out' over the week. They could then have sensed a gradient in the moisture content of their surroundings and moved towards it. Mechanisms in animals' bodies can give animals responsive behaviour, as seen here. For instance, C. elegans uses its cGMP pathway, neurons and biochemistry to respond to water content with movement (Wang et al., 2016).
References

Wang et al. (2016). cGMP Signalling Mediates Water Sensation (Hydrosensation) and Hydrotaxis in Caenorhabditis elegans.

Gendron, R. P. (1977). Habitat selection and migratory
behavior of the intertidal gastropod Littorina
littorea. J. Anim. Ecol 46 79-92


text:
What are those patterns found on the surface of wooden furniture? Are those growth rings of trees?
This image can give a suitable example for the above question.

Which pattern the long lines are the separations between the individual boards.

*or; The streaks present on the top face of the table.

that is what I was talking about.

Just checking: you mean wood grain? As seen in https://commons.wikimedia.org/wiki/Category:Wood_grain#/media/File:16_wood_samples.jpg? (This shows a 4x4 grid of wood samples, each one shows a different wood grain pattern.)

Thees cut on any angle will reveal growth patterns; not all wood grows exactly the same. Some kinds grow straight and have a very even grain, at the other end is the "black gum", the grain of which seems to follow no organized pattern (it's almost impossible to split.)
Without a close up, it's hard to say exactly what's going on with your table.
Some woods, because of their grain and even density, take up stain very evenly and uniformly. An example would be oak. Some woods take up stain more irregularly, an example being maple.
Your table, though (all this is speculation since there's not a close up or head on view) looks like an example of blotchy stain uptake.
This is an example of blothcy staining wood:

If you look carefully at the grain, you can see that's not the only cause of uneven uptake. Some blotchiness is due to not sanding the table down finely enough. Some is due to the uneven density of the wood. See that diagonal scratch? It takes up color regardless of the grain. As do the ends of the boards.
Your table is made up of younger trees (you could see growth rings on the edge) which will give you more uneven uptake, plus it's a blotchy job. So, the answer is yes and no. Or, a qualified yes.