text:
Do presynaptic neurons and postsynaptic neurons have different compositions of neurotransmitter receptors and transporters?
For example if certain neurotransmitter is released, will there be neurons that won’t be even potentially affected, because it doesn’t have such type receptors?

Typical bouton-spine synapses are formed as an active process between the pre- and post-synaptic cells, there is communication between them through structural proteins, etc. Therefore, as part of the normal developmental process, usually postsynaptic cells will have receptors for the major neurotransmitter released by the presynaptic cells. However, some neurotransmitters are released more broadly into the extracellular space rather than at highly specialized synapses: in this case, the neurotransmitter is not likely to have an effect (or the same effect) on all nearby dendrites.

@BryanKrause - that would be an excellent answer.

@AliceD Took me some time to get back to this and compose a properly-cited answer.

Typical bouton-spine synapses are formed as an interactive process between the pre- and post-synaptic cells (Scheiffele, 2003). There is communication between pre- and post-synaptic cell through guidance cues, growth factors, and structural proteins, as well as neurotransmitter release itself. Therefore, as part of the normal developmental process, postsynaptic cells will usually have receptors for the major neurotransmitter released by the presynaptic cells: they find each other rather than connecting at random.
Synapses that become inactive or have lower activity than their neighbors can also degrade and disappear entirely (Purves and Lichtman, 1980) by a competitive process (Balice-Gordon and Lichtman, 1994). Because of this process, I would expect that even if some developmental fluke led to a formation of a synapse between mismatched pre/post neurotransmitter release/receptors, the result would be that the synapse would get no stimulation and would be pruned according to the normal process.
However, some neurotransmitters can be released more broadly into the extracellular space rather than at highly specialized synapses (including serotonin, dopamine, and acetylcholine - note: these neurotransmitters can also be released at synapses) (De-Miguel and Trueta, 2005; Trueta and De-Miguel, 2012) and call also 'leak' from synapses into the extrasynaptic space: in these cases, the neurotransmitter is not likely to have an effect (or the same effect) on all nearby dendrites, only those that express fairly high-affinity receptors that can detect the neurotransmitter at an extrasynaptic concentration.
References:
Balice-Gordon, R. J., & Lichtman, J. W. (1994). Long-term synapse loss induced by focal blockade of postsynaptlc receptors. Nature, 372(6506), 519.
De-Miguel, F. F., & Trueta, C. (2005). Synaptic and extrasynaptic secretion of serotonin. Cellular and molecular neurobiology, 25(2), 297-312.
Purves, D., & Lichtman, J. W. (1980). Elimination of synapses in the developing nervous system. Science, 210(4466), 153-157.
Scheiffele, P. (2003). Cell-cell signaling during synapse formation in the CNS. Annual review of neuroscience, 26(1), 485-508.
Trueta, C., & De-Miguel, F. F. (2012). Extrasynaptic exocytosis and its mechanisms: a source of molecules mediating volume transmission in the nervous system. Frontiers in physiology, 3, 319.

Nice one +1! I tried to find an answer for this to no avail. Intuitively I expected something in the line of your answer, but I couldn't back it up constructively.  Awesomeness.


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Are humans Gnathostomates?
Gnathostomates are vertebrates having jaws. But when I search on the internet for Gnathostomates, I always find out that they are sharks and fish-like organisms.
But are humans not also Gnathostomates? Don't we have jaws?

Humans are fish-like organisms.

Absolutely, humans belong to the superclass Gnathostomata. It's simply the class of jawed vertebrates, and includes 99% of vertebrates.  It also includes the class Mammalia, which includes humans.

For basic and fairly light reading, check out Wikipedia on Gnathostomata and Mammalia.

What's a stem group and a crown group?

TIL: Snakes are Tetrapoda.

@user28434 Absolutely. Pythons and boa constrictors, for instance, still have vestigial hind leg bones hidden within their muscles. They also have tiny buds sticking out where their hind legs used to be. See, for instance, the first paragraph and image here.

Nitpick: It's mammalia, from Latin mamma, old greek μάμμη for breast or (baby-talk) mother.

Yes, all jawed vertebrates belong to the infraphylum Gnathostomata, including all mammals (and therefore all humans).
Here are 3 different taxanomic trees showing this:

 Source: Wikipedia

 Source: UCL

 Source: INTECH

Yes of course Humans are Gnathostomes. Under division Gnathostomata you have 2 Superclasses that include Pisces and Tetrapods. Under Tetrapoda are 3 classes- reptiles, Aves, mammals. So Humans are indeed Gnathostomes.

Taxonomically humans have been grouped as mammals placed under superclass Tetrapoda (Includes amphibians, reptiles, Aves and mammals) being different from  other superclass Pisces which includes sharks and bony fishes. All the animals placed under superclass Pisces and Tetrapod are have been grouped as gnathostomes characterised by the presence of jaws in their mouth. In contrast all animals which do not posses jaws like lampreys and hagfishes (primitive jawless fishes) have been grouped as agnathans.Both gnathostomes and agnathans have been grouped as vertebrata (sub phylum) and as Chordata (Phylum) groups.
Source : Vertebrates: Comparative anatomy, function & evolution  By Kenneth V Kardong

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


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Hayflick's limit and cell division
Suppose the Hayflick's limit of a cell is 10 and it divides 10 times.  At this point, it undergoes differentiation.  Is it possible for it to undergo dedifferentiation at this point?

I don't think so naturally. I think the general stream of the progeny goes stem cell => pluripotent cell => progenitor cell => specialised cell.

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Why can't complex multicellular organisms reproduce by regeneration?
My textbook says that regeneration isn't  possible in complex multicellular organisms.
But why? Why can't specialized cells be present in the bodies of complex multi cellular organisms which can proliferate and ultimately make a whole new organism, when (for example) cut in two?

What textbook are you using?  Regeneration most assuredly is possible in many complex multicellular organisms, such as the Asteroidea of the Echinoderms.

The book means to say in most organisms

I was doing some research on this myself and from what I had found, the body has hox genes that direct the formation of body parts. So now the obvious question is that if a body part contains stem cells and hox genes, shouldn't it be able to regenerate a new body? Well, perhaps. But the problem is that as organisms become more complex, the process of the creation of their bodies also becomes more complex. For example, in the fruitfly, if the labial gene function is not expressed, the mouth and head that develop outside the body do not get involuted and that prevents the salivary gland from forming.
So the answer about why multicellular organisms can't regenerate so easily simply seems to be because the process of creating a multicellular body has for some reason become an extremely complex, intertwined process where various body parts creation is dependent on other body parts creation. So in the evolutionary process it's entirely possible that the stem cells noted that there's no point trying to regenerate a body part, and therefore they just don't.
Here's an anomaly. There's a jellyfish that can reverse aging and go back to infant stage. I think it's able to do so because it has a simple body structure.
Another possible reason could possibly be the presence of unstructured proteins which are more abundant in multicellular organisms.

The jellyfish you mentioned is turritopsis dohrni if I remember correctly. When I was young, I wanted to be like that jellyfish. Now I know that im too 'complex' (instead of simple) to be that.

An evolutionary reason for the lack of regeneration in long lived animals is cancer. The waiting undifferentiated cells (stem cells) are another potential source of cancer.

Not all complex organisms are incapable of regeneration!
The most famous example is probably the axolotl - a salamander that is able to regrow whole limbs or even parts of essential organs like the brain or heart. While it's not yet know how that is possible, there are a lot of researchers looking into it (the genome of this species was fully sequenced last year).
Another example is the regeneration of zebrafish fins, which - while less impressive - is by now pretty well studied.

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From which end of mRNA does transcription start?
The book "Understanding bioinformatics", says that "RNA polymerase transcribes the anticoding strand in the direction from 3' to 5', so that the mRNA strand is produced from the 5' to the 3' end".
But from Khan Academy's article, I got "RNA polymerase builds an RNA strand in the 5' to 3' direction, adding each new nucleotide to the 3' end of the strand". Also "the codons of an mRNA are read in order (from the 5' end to the 3' end)". Which one is correct?

@Thymine's answer is correct. I just thought I'd post a more graphic answer for clarity.
                  <==(RNA Pol)3'------------------------- 5'
5' ------------------------------------------------------ 3'
3' ------------------------------------------------------ 5'

The RNA Polymerase is synthesizing on the 3' to 5' strand, but nucleic acids are always added in reverse direction to the template strand (this goes for DNA replication as well as RNA synthesis).
The confusion arrises, of course, because there are several different ways of looking at it.  If you're looking at the polymerase's template strand, you would (like the book) that the RNA Pol is synthesizing 3' to 5'.
On the other hand, if you're looking at the strand being synthesized, you'd say (like Kahn Achademy) that it's being synthesized 5' to 3'.  This is why Kahn says

[...] adding each new nucleotide to the 3' end of the strand.

There is an incomplete mRNA fragment with the RNA Pol sitting on the 3' end.  That's where it adds each new nucleotide.

They're both correct. The confusion stems from the book talking about the anticoding strand as well as the newly-formed coding RNA strand, whereas Khan Academy talks only about the coding strand.
From the book:

The anticoding strand is transcribed from 3' to 5'.
  Therefore the coding strand is produced from 5' to 3', meaning the very first nucleotide added by the RNA polymerase is the 5' end, and you add to it in the 3' direction.

From Khan Academy:

The RNA polymerase produces a strand of RNA from 5' to 3'.

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Where does Embryo Implantation occur?
Where does the embryo get implanted? If it is in the uterus side wall, why is the embryo shown hanging from top in some pictures?

According to Minami et al. (2003)1 (open access) the early gestational sac can be located by ultrasound, and usually is high in the uterus, more often on the left or right than in the middle.  They provide an illustration of the distribution.

 1. Minami, S., Ishihara, K. and Araki, T., 2003. Determination of blastocyst implantation site in spontaneous pregnancies using three-dimensional transvaginal ultrasound. Journal of Nippon Medical School, 70(3), pp.250-254.


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How to attract Cyanobacteria?
I would like to attract cyanobacteria in one spot on an object (e.g. cloth,) instead of having it swim in the media. my current method is to pour it on the object in a beaker and wait for some of them to become attached (very pour attachment yield).
Now, I am thinking of making the object emit light. Do you think that the bacteria will swim all the way to the cloth because there are attracted to light?
is there a better method to help the bacteria get attached to the cloth?

Do you have more details about the experimental setup and constraints? E.g. is your goal to deplete cyanobacteria from a sample? Or to observe the diversity of cyanobacteria in a sample? How pure must the product be (is it a problem if you attract other bugs than cyanobacteria as well)? Can you modify the cyanobacteria, if it's a laboratory strain? And so on... we need as much detail as you can provide to give you an accurate answer!

It might work, many cyanobacteria are reported to be phototaxic. https://www.pnas.org/content/115/52/E12378

We're looking for longer, self-contained answers. It's important to refer to external resources, but your answer will be better received if you can summarize the key points from a source that are relevant to the question asked so that your answer itself is informative beyond just a link.


text:
How does the original ionic distribution restore after synaptic transmission
During synaptic transmission the calcium ions around the presynaptic membrane diffuse in due to the influx of Na+ ions and the resulting depolarization. This happens because the calcium channels are voltage regulated ones. At the same time on the other side of the membrane there is efflux of K+ ions in order to repolarize the membrane. My question is how does the original ionic distribution restore which is more K+ on the inside and more Ca2+ on the outside? What kind of pump does this job and what is the exact mechanism? As contrast to the nerve membrane where the Na+/K+ pump does this. I don't find a pump like K+/Ca2+ pump to do this.

Most of the depolarization in the presynaptic terminal is still sodium-based, it's just that there are also calcium channels there. Very little calcium actually moves, as these channels are closely coupled to the synaptic release machinery (see for example Stanley 1993 Single calcium channels and acetylcholine release at a presynaptic nerve terminal).
The calcium concentration gradient has to be established everywhere in cells that have this gradient (all animal cells, as far as I know), not just at a synapse, since calcium is typically a powerful "second-messenger" signal.
The two common mechanisms for transport are by using the gradient of sodium via calcium antiporters (this mechanism: using sodium or proton gradients to move other ions/molecules, is quite ubiquitous in biology), and via a calcium ATPase. Calcium transport involves both the external space and intracellular calcium stores such as within the endoplasmic/sarcoplasmic reticulum.
In the short term, calcium concentrations are also dealt with via chelation by calcium-binding proteins.

What about K ions . Is their level is maintained by simple diffusion of K ions or some special type of transporters or ATPase come into action. Anyways thanks the links were of great help

@Ubaid You've already mentioned the Na/K ATPase - that's the primary way that K concentrations are maintained.


text:
Trying to identify an insect
Toady a friend saw an insect in his garden, in the UK (England).
It looks like a combination of a hover wasp, a wasp and a dragonfly. Whist flying, I'd describe it more similar to a dragonfly.
I've used Google images to try and identify it, and come close, but the creature was about 3 inches long and up to 1 inch wide. I thought it was a broad-bodied chaser but he assures me (possibly incorrectly) it wasn't big enough

I would agree with you on this one - looks like a female or young male Libellula depressa (the 'broad bodied chaser') to me. It has the characteristic broad, flattened abdomen and the distinctive brown-yellow abdomen with bright yellow patches and the dark wing bases are both visible (the latter only just, to be fair). The broad abdomen differentiates it from the other Chaser and Skimmer dragonflies while the colour is quite distinctive (the species is sexually dimorphic; mature males have a blue abdomen while females and young males have a yellow abdomen). Not sure what you friend is talking about regarding the size; 3in long is about right for L. depressa. It's in the right geographical region too.
(thanks to @RHA for pointing out to me that young males also have yellow abdomens!)

Citation from Wikimedia Commons: By No machine-readable author provided. Bogdan assumed (based on copyright claims). - No machine-readable source provided. Own work assumed (based on copyright claims)., CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=754252

You are correct, this is undoubtely libellula depressa. However, immature males lack the characteristic blue color and look the same as females. So it can be a young male as well.


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What are the different types of helices in protein secondary structures and how do they differ?
What are the different types of helices in protein secondary structures and how are they differentiated?
In the DSSP docs, types of helices mentioned are: Alpha-Helix, Helix-3, and Helix-5.
In the STRIDE docs, types of helices mentioned are: Alpha-Helix, 3-10 Helix, PI-Helix.
Why does DSSP have Helix-3 and Helix-5, while STRIDE has 3-10 Helix and PI-Helix - are they different expressions for the same thing?
What are the differences between these types of helices, what are their full scientific names so that I could read more about them, and are there any other types of helices not mentioned here?

This DSSP page makes it clear that:

Helix-3 = 3-10 helix
Helix-5 = π-helix

The α-helix is described in every biochemistry text book and widely on the web. It has 3.6 residues per helical turn and has 13 atoms in the ring formed by the hydrogen bond and so can also be called a 3.6-13 helix.
The 3-10 helix is less common than the α-helix, but is still widespread. By analogy with the alternative nomenclature just described for the α-helix, it has 3 residues per helical turn in a 10 atom ring.
The π-helix is even less common. It is a wider helix with 4.6 residues per turn.
A comparison of the three can be found in this proteopedia article, from which I have taken the illustration below.

There is also the collagen triple-helix, but that is specific to collagen, whereas the others are general examples of secondary structure found in many proteins.
Standard Nomenclature
There is no such thing as a “full scientific name” in this area of molecular biology. Names tend to get standardized by unofficial agreement when ambiguity becomes a problem. Helices other than the α-helix are not very well known, but the terms 3-10 helix and π-helix are certainly more common than Helix-3 and Helix-5, which I suspect may have been a computational convenience. However, an internet search indicates that for scientific journals 310-helix is generally preferred to 3-10 helix or 3(10)-helix, these latter perhaps reflecting work in a plain text environment or the word-processing or HTML limitations of writers.


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How can a homozygous mutation, considered pathogenic, occur on a gene such as HFE without the disease developing?
What happens when you have a homozygous mutation on a gene (eg. a swapped base), that is considered pathogenic, but without developing the disease?
It it were a heterozygous mutation I would get it, because we still have at least one healthy/wild-type copy of the gene, so at most the disease will just manifest in a more mild form, but with a homozygous I have no idea how is it possible to NOT develop the disease.
Also, what happens when heterozygous mutations develop the disease? In these cases why does the healthy version of the gene goes "quiet"?
One example is HH caused by HFE gene mutation (mostly C282Y and H63D), and not everyone develops the disease, doesn't matter if they are heterozygous or homozygous.

What happens when you have a homozygous mutation on a gene (eg. a swapped base), that is considered pathogenic, but without developing the disease?

It may be an example of incomplete penetrance of variable expressivity. Simply, you are probably dealing with a complex trait in which either more than one gene is involved, or there is interaction between genetics and envronmental factors.

Also, what happens when heterozygous mutations develop the disease? In these cases why does the healthy version of the gene goes "quiet"?

I assume you are still talking about a putatively recessive disease. One possible explanation is haploinsufficiency, i.e. the WT allele alone doesn't produce enough transcript and the heterozygous individuals has "problems"

One example is HH caused by HFE gene mutation (mostly C282Y and H63D), and not everyone develops the disease, doesn't matter if they are heterozygous or homozygous.

And indeed HH is an excellent example of complex disease, in which genetics is involved, but the inheritance is not purely Mendelian.


text:
Function of Smooth Muscles in the skin
I understand that the overall function is voluntary movement, but is it the same in the skin? Is the main function in the skin movement or is there a greater function? Could anyone could provide this information or at least recommend a site that could help me with this research, as I have been searching and I haven't been able to find the answer?

Smooth muscle in the skin actually produces very little motion.  They are found in special places, such as the areolas of the nipple, the tunica dartos of the scrotum, and also around hair follicles.
Smooth muscles that surround hair follicles give you what is known as goosebumps - they contract all together, creating a bump in your skin around the hair follicle.  This can happen when you're cold, scared, or experiencing strong emotion.

Sources:

Skin Tissue Engineering and Regenerative Medicine, Justine Fenner, Richard A.F. Clark, 2016; Chapter 1


text:
Can oxytocin travel from one cell to another via gap junctions?
Oxytocin is a 9-residue secreted peptide. As a hormone, can it travel through gap junctions, assuming that it is stored in pre-synaptic neuronal vesicles?

Synaptic vesicles are on the order of tens of nanometers (for example Zhang et al give a mean diameter around 40 nm).
Gap junctions are much smaller, on the order of 1-2 nm. Maeda et al measure one at 1.4 nm.
Peptides the size of oxytocin present in the cytosol could theoretically travel through gap junctions. Vesicle-packaged peptides or molecules of any size cannot.

Maeda, S., Nakagawa, S., Suga, M., Yamashita, E., Oshima, A., Fujiyoshi, Y., & Tsukihara, T. (2009). Structure of the connexin 26 gap junction channel at 3.5 Å resolution. Nature, 458(7238), 597-602.
Zhang, B., Koh, Y. H., Beckstead, R. B., Budnik, V., Ganetzky, B., & Bellen, H. J. (1998). Synaptic vesicle size and number are regulated by a clathrin adaptor protein required for endocytosis. neuron, 21(6), 1465-1475.


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How to design the primer when you don't have GC?
I have treated my RNA with sodium bisulfite so all my cytosine is converted into thymine. Then I used that RNA for my RT reaction. I have a cDNA template without Cs. Now I am trying to amplify that region with PCR.
For some reason I am not able to amplify the region. I designed my primer by Primer 3 plus and manually, but it is not working. The main reason is that I don't have GC pair in the primer.
Is there any other way to fix the problem?
My primer concentration is 200nm.

Are you sure all the cytosines in your RNA were converted to thymines? These assays are usually done to determine which bases are protected by binding to other macromolecules or to secondary structures in the RNA. 2) Even if you converted all Cs to Ts you would still have Gs that will pair with Cs when you make the first strand of cDNA — thus, saying there are no GC pairs can't be correct. 3) It might also help if you included the expected original (pre-bisulfite treatment) primer binding sequence.

yes, all the Cs converted into Ts, i amplified the very short region then i confirmed by sequencing. In the genome there are some Cs are methylated i want to target them. My question is within the primer I don't have GCs. My primer is not annealing properly i am getting only Primer-Dimer.

Without the sequence information I can only give very general advice.
1) Pick a different location — primers generally work best when they have something close to 50% GC content.
2) Make sure the 3' ends of your primers aren't complementary.
There is detailed advice on how to design effective primers available online including:

from MIT
Dieffenbach, C. W., Lowe, T. M., & Dveksler, G. S. (1993). General concepts for PCR primer design. PCR methods appl, 3(3), S30-S37.

Somehow i managed to amplify the region of interest. I used HIFI-Kapa PCR mix. I kept


text:
Helix aspersa or Cornu aspersum
The common garden snail was originally assigned as Helix aspersa and stayed that way for over 200 years. Recently, some biologists assigned it to the genus or subgenus Cornu renaming it to Cornu aspersum, yet other researchers assigned it to Cantareus. Still, many texts still use the name Helix aspersa.
My question is what is the correct or official binomial nomenclature (scientific name) of the garden snail as for 2019?
Remark: I read Wikipedia but even there there are inconsistencies about it. E.g. Wikispecies.

I consulted with Prof. Henk Mienis, the curator of the Israeli Mollusca Collection, and the valid name is Cornu aspersum. The Israeli subspecies is Cornu aspersum megalostomum.


text:
Why don't chromosomes double in S-phase?
DNA doubles in S-phase, but chromosomes don't double in S-phase, in spite of the fact that chromosomes are formed by the condensation of DNA. Why is this so?

My answer won't be precise, so I post it as a comment. It's a question of terminology, and it's normal to be confused: a chromosome can have one or two chromatides, but we can talk about a single chromosome in both states. For less confusion, we could talk about a replicated chromosome when one chromosome is composed of two chromatides. But I'm looking forward for a better answer than mine, since I'm still a student myself and don't exactly know why we call them like that.

First, chromosomes are composed of an original and a replicated chromatid, called sister chromatids. Chromatids are composed of tightly packed DNA.
DNA is replicated after the end of the S-phase, or in other words, the material composing the two sister chromatids is there. The catch is that chromosomes and chromatids aren't actually condensed yet, the DNA is still completely unpacked at this stage. So in fact, while you do not see actual chromosomes, the material composing them has been duplicated during the S-phase.
DNA condensation occurs two steps later during the prophase, where distinct sister chromatids/chromosomes are then formed from the packing of DNA that was duplicated during the S-phase.


text:
What does the placenta consist of?
It includes the basal plate, the pool of blood between the chorionic plate and the basal plate and the chorionic plate, what else?

Why isn't anyone giving an answer

Possibly because the question seems like it could be easily answered via Google, and because you haven't demonstrated that you've made any effort to answer it yourself yet. Putting it another way, what do you think the answer is? What is blocking you from researching this yourself?

You could’ve easily googled this, but anyway...
Placenta is a composite structure made of embryonic and maternal tissues.
The placenta is composed of: The chorion, which is the embryonic-derived portion of the placenta. Chorion contains the trophoblast cells (cells that make up the outer cell layer of the blastocyst). finger-like structures called chorionic villi are also present in the placenta. Lastly, the space in the placenta that surrounds the villi and the maternal blood is called the intervillous space.
Source: https://study.com/academy/lesson/the-placenta-and-the-fetus-structure-and-function.html


text:
Reading genotype aloud
For this genotype, P2ry12$^{+/+}$ I read it "P2ry12 wild type." For animals with the GFP being expressed under one Cx3cr1 promoter, Cx3cr1$^{+/GFP}$, how do I read that aloud?
What about for: Cnr1$^{flox/flox}$, Cnr1$^{flox/+}$, Cx3cr1$^{CreER/CreER}$, and Cx3cr1$^{CreER/+}$ mice?
I'll give my attempts below and take suggestions:
Cx3cr1$^{+/GFP}$ "Cx3cr1 wild type with heterozygous GFP expression" or "Hetero GFP expression" or "GFP" as in for P2ry12$^{+/+}$, Cx3cr1$^{+/GFP}$ animals it would read "P2ry12 wild type with GFP" to reduce redundancy if it is clear to the listener.
Cnr1$^{flox/flox}$  "with Floxed Cnr1"
Cnr1$^{flox/+}$ "with hetero floxed Cnr1" Would the words incomplete or partial ever be appropriate here? As in "a partially floxed Cnr1?"
Cx3cr1$^{CreER/CreER}$ "homo CreER under the Cx3cr1CreER promoter" or just "the CreER animals"
Cx3cr1$^{CreER/+}$ "the hetero CreER animals"
and for CreER is it correct to say that is a chimeric protein of Cre and mutated hormone-binding domain of the estrogen receptor?
Thank you in advance!
Edit:
I do see that one of them is clarified by the authors: P2Y12-deficient (P2ry12$^{–/–)}$ GFP-expressing mice.

For something like this, just try your best to describe what it is. I don't think there's a definitive way to do this.

For Cx3cr1 +/GFP +/+:

"Cx3cr1 heterozygous with GFP expression" is the most accurate.
"Hetero GFP expression" works if it's clear you're referring to
Cx3cr1.

Cnr1 flox/flox +/- +/-:

"Cnr1 floxed" or "homozygous for floxed Cnr1" are both good.

Cnr1 flox/+ +/- :

"Cnr1 heterozygous floxed" works well.

Cx3cr1 CreER/CreER +/+ +/+:

"Cx3cr1 CreER homozygous" is cleanest.

Cx3cr1 CreER/+ +/- :

"Cx3cr1 CreER heterozygous" is perfect.

CreER is a chimeric protein combining Cre recombinase with a mutated estrogen receptor domain. This makes it activatable by tamoxifen administration.

Can you please explain the notation you used in these? For example: the "+/- +/-" in "Cnr1 flox/flox +/- +/-."

Thank you for your answer by the way! It was very helpful. I am reading them now from left to right and adding heterozygous or homozygous on the end accordingly.


text:
Translating either rs number or genomic position to either a residue in the DNA or in the amino acid sequence
Studying Schizophrenia and reading some papers discussing polymorphisms in the 5HT-2A receptor gene (HTR2A). Specifically, the authors mention A-1438G, T102C, his452tyr. How does one best take processed genetic data, such as on 23andMe, or the entire raw data with Nebula to determine which variants are carried? 23andMe allows access to raw data and you can search for the gene by HTR2A where there is a list of rs markers such as rs9595552 and rs17069218 and their genomic positions 47407430 and 47408350, respectively. How do I take A-1438G, T102C, his452tyr and relate them to either the rs number or genomic position? Supposing they aren't on the list and I get a whole-genome sequencing done by Nebula, how would I go about finding these residues? I know that HTR2A is on chromosome 13q14-21. I understand the first part 'chromosome 13', but not the rest. Nor do I understand how I would go about navigating the raw genomic data.
Edit:
Luckily, I was able to use Google to track down these relationships.
rs6313 = T102C
rs6311 = A1438G
rs6314 = his452tyr
when I looked to the data on 23andMe, online it yielded:
rs6313 = T102C ; A or G ; AA
rs6311 = A1438G
rs6314 = his452tyr ; G or A ; GG
I was able to download the complete raw data and search the text file for the middle one yielding:
rs6313 = T102C ; A or G ; AA
rs6311 = A1438G ; TT
rs6314 = his452tyr ; G or A ; GG
Now the last one appears apparent. We are clearly discussing the amino acid sequence. Histidine (H) has two possible codons, CAU and CAC. Tyrosine has two possible codons, UAU and UAC. Meaning that the variation lies in the first position, with a G in the DNA yielding histidine and an A giving tyrosine. So G or A is what we are looking for in the DNA sequence from 23andMe and all is well.
If we then try and apply this same process to the other two polymorphisms, assuming they are amino acids and not nucleotides, it doesn't work.
alanine(A): GCU, GCC, GCA, GCG
glycine(G): GGU, GGC, GGA, GGG
threonine(T): ACU, ACC, ACA, ACG
cysteine(C): UGU, UGC
For alanine/glycine, the nucleotide variation would be occurring in the second position, G/C. Yet the 23andMe data says genotype is TT. Therefore I believe it is correct to assume A/G is referring to nucleotides in the DNA.
The same would apply for threonine and cysteine, for two out of three of the nucleotides must be the same and this is not the case. Assuming instead they are nucleotides is compatible with the data from 23andMe; A or G and AA.
That being said, I am aware that the promotor does not always lie at the beginning of a gene, but I do not know where else it can lie. Can it lie at the end? A-1438G is in the promoter, T102C in exonI, and his452tyr in exonIII. Converting his452tyr we have (452*3-2=1354) G-1354A. Putting them in order: exonI T102C, exonIII G-1354A, promoter A-1438G. Does this sound correct?

I'm not exactly sure what you're asking for, perhaps you could structure your question a little better. But searching for your gene at dbSNP seems like a good start. That lists you all gene variants currently mapped to the specific gene. Example: https://www.ncbi.nlm.nih.gov/snp/?term=HTR2A. After searching you can also click Varview to view the genome position of the gene and all its variants.

If you go to the gene at Genbank you will see that the gene has a few variants, which are based on differing intron/exon boundaries. The 13q... is the position based on karyotype analysis. You can relate this to straight genome positions to some extent, but you would need to determine the start codon and the intron/exon boundaries for your encoded protein.
There are a few possibilities:

The positions are amino-acid substitutions - They are related to the genomic sequence by the coding position starting with the start codon ATG (Met) and working from there. In this case it would be Alanine to Glycine at amino-acid 1438 of the protein sequence. However, if you look at the CDS regions and go to the linked proteins (/protein_id=NP_XXXXXXXX) you will see that there are only 430ish amino-acids in the sequence. The His425Tyr is certainly an amino-acid substitution of this sort, the others might not be.
The positions are raw coding positions. A highly conserved single base substitution at the designated site. This would be for the coding sequence only. You would take the exons only and count bases from the A of the start ATG.

I've not tried to access the 23-and-me data, so I don't know how it works, but the genomic position will be starting from the first base in chromosome 1 and counting up I think. Generally data of this sort will be analysed using a specific set of tools in a bioinformatics system.

Thank you for your answer, bob1. I updated the original post if you can check my work that would be helpful. I may have to update the post in the future if there is an instance where Google does not yield a rs number for the polymorphism in question.


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Is the use of DNA SNPs vs amino acid variations in the description to detail the absence or presence of a consequent amino acid variation?
Studying Schizophrenia and reading some papers discussing polymorphisms in the 5HT-2A receptor gene (HTR2A). Specifically, the authors mention A-1438G, T102C, his452tyr.
Was his452tyr not described as A-1438G and T102C, in terms of a DNA SNP, because the variations in A-1438G and T102C do not give rise to a different amino acid? Histidine is coded by CAU, CAC, and tyrosine by UAU, UAC. The first position in the mRNA sequence accounts for the variance, and hence the first position in the DNA sequence. In other words, it could have been described as G-1354A (if I did that right U->A and C->G and (452*3)-2 to give the 1 position). Or is this typically a matter of original author preference, or perhaps for amino acids that would significantly change the protein?


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is there any kind of paw/pads lines or paw muscle anatomy in animal hands?
just like in the title my question is, is there any kind of paw/pads lines or paw muscle anatomy in animal hands? or its pretty much random?
example like mammary lines as bilateral structure that rules where mammary tissue can develop. is there similar thing like this for animal paw/pads? especially comparable to human hands?
prefferably include image (example like this mammary lines) if possible.

Do hands have developmental pathways, yes there are a lot of them, listing them all would be pushing it for a single question.

@John a link is fine too

try starting here https://www.ncbi.nlm.nih.gov/pubmed/19553860 and https://emedicine.medscape.com/article/1287982-overview

@John so far as i read and search the link you provide, none of them talk or has anything resemble about paw/pads though, im not talking about the hands generally but specifically about the paw/pads but not exactly about human palm either if its not clear.

human hands and forepaws are the same thing, there really is no formal distinction.  they are all controlled by the same developmental pathways.


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Is a gametophyte a spore?
The male and female gametophytes are pollen and embryo sacs respectively. I wondered if they are spores as their brethren are meiospores.

No.
But close.  Very close.  Basically, a gametophyte is a spore that has / is undergoing mitotic division.  Therefore, it is still haploid, having not undergone fertilization yet, but it is no longer a dormant, unicellular spore; it's passed into the new phase of gametophyte.
The gametophyte produces sexual organs which produce the gametes that will actually be used in fertilization.  Two gametes fuse, at which point, a diploid cell is produced (called a zygote, just as in animals).

The meiospores are the spores you see in the picture on the far left: they are dormant, unicellular, haploid spores, which will turn into the gametophytes.  (meio + spores; spores that have undergone meiosis)

Sources:

Meiospore, Biology Online
Gametophyte, Wikipedia
Plant Life Cycles, Developmental Biology, 6th ed.
Spore, Wikipedia


text:
Does a cell deprived of growth factors undergo apoptosis or G0 stasis?
I can't seem to find a decisive answer on this topic in any of my textbooks. If a cell is deprived of growth factors does it:

Activate apoptosis
Go into the G0 phase but keep living?

Thanks.


text:
When is gene density an important parameter in experiments?
As per wikipedia definition, gene density is defined as:

"In genetics, the gene density of an organism's genome is the ratio of the number of genes per number of base pairs, usually written in terms of a million base pairs, or megabase (Mb). The human genome has a gene density of 12-15 genes/Mb, while the genome of the C. elegans roundworm is estimated to have 200."

But I would like to know in what circumstances one would consider gene density as an important parameter? To be specific in what kind of experiments the model organism's gene density plays key role?

I don't know about experiments, but it might be useful in estimating size of exons & predicting length of mRNA.

Of the top of my head two fields that could make use of gene density arw Bioinformatics and evolutionary studies. Gene density says something about complexity of organism, information storage, etc

"Note that interaction effects among genes also depend on their physical distance." I think that's more of a pragmatic assumption, because we tend to associate regulatory features with their closest downstream TSS, though it's certainly not a hard and fast rule. e.g., in certain organisms like budding yeast, its known that the most transcription factor binding sites are downstream of gene bodies. even in humans, the association is not entirely clear as there are both cis and trans effects especially notable with things like super enhancers and things of that nature. Or consider the following, http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004461

This is an open-ended question and will be impossible to correctly answer. I am voting "to close as too broad". Note also that the question in the title is not the same as the question in the post.
But I still wanted to give you some information that may help you. Here are just a few examples for which knowing gene density matters.

Background selection is the process by which purifying selection reduces heterozygosity at nearby loci. Knowing the density (and positions) of genes (and other sequences potentially under selection such as regulatory sequences) is essential to understand the variation of background selection throughout the genome. Being able to design maps of variation of background selection throughout the genome is essential to improve our ability to detect local adaptation and positive selection as background selection leaves similar genetic signature.
The evolution of the genome size is in itself of interest to evolutionary biologists. Species having large genomes ave large genomes mainly due to repetitive neutral sequences. As such the question of gene density is essential to understand the evolution of genome size.
The gene density varies throughout the genome (with a variance greater than the mean, that is it does not follow a Poisson distribution). Understanding the evolution of gene density at different regions is of interest to many. Note that interaction effects among genes also depend on their physical distance.


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How can the organic mercury compound Thiomersal be not dangerously toxic?
My intuition tells me that organic mercury compounds are absolutely toxic. Unimaginably, fundamentally, extremely and uncompromisingly toxic.
I know that is not true for all doses.
Thiomersal is the organomercury compound that was used in vaccines as preservative. It's use has been controversial outside of the scientific community.
I am not asking whether the use in vaccines is dangerous, to be clear:
The use of mercury as Thiomersal in vaccines it is not dangerous.
That is well-established beyond reasonable doubt. Far beyond.
My intuition tells me that any organomercury compound it so mind-blowingly toxic that I feel cognitive dissonance if I try to accept that, at some dose, it's not.
I'm totally aware that toxicity depends on dose, that the compound is toxic at higher doses, and the dose used is just low enough that it is not toxic.
But the dose used is still antiseptic and antifungal, and having anything in my body that contains mercury and carbon in a dose high enough to kill a form of life feels just not right.
I would not worry at all to get vaccinated with a vaccine containing Thiomersal, and if a physician would ask me whether I prefer a vaccine with or without it, I would answer "Whatever you think is best."
But still, on the abstract level, the feeling of "That can't be right" to have an organomercury compound in my body it pretty strong.
I know it is not dangerous, but:
How is that even possible?

How is it possible to have highly toxic chemicals like sodium and chlorine in the body?  Or how can harmless carbon and nitrogen form highly toxic cyanide?

@jamesqf I understand what you mean, and my intuition has no problem with that, even cyanide itself can be used as medical drug. But organomercury compounds are much worse than even cyanide: For example, methylmercury goes into the brain and stays there, going on to kill brain cells until there are not enough to live, some month later. Cyanide makes getting oxygen not work, either you die, or feel bad until the next day and all is fine, roughly. Methylmercury is just unimaginable toxic.

I think you missed my point, which is that chemical compounds have chemical properties that are usually entirely unrelated to the properties of the elements that compose them.  The properties of CN, including its toxicity, are nothing like those of elemental C or N.  NaCl (necessary for life) is nothing like elemental Na (probably bursts into flame in contact with body fluids) or Cl (used in WWI as a poison gas).  So why should any particular mercury compound be toxic?  See answer regarding the difference between ethylmercury &  methylmercury.

You might also ask why it is that literally hundreds of millions of people can spend large parts of their lives with mercury-containing dental amalgams in their teeth, without showing any sign of mercury poisoning.

@jamesqf And why sailors used to ingest large globs of pure metallic mercury, aka quicksilver, to clear intestinal blockages. Not that it's recommended as it can cause long-term mental effects, of course...

@jamesqf I see what you mean, and agree, the elements in a compound have no relation to the toxicity. But there are classes of compounds that are typically toxic. For example the lower alcohols. And with mercury, the organic compounds are such a class. It's enough to be toxic if only minor amounts of a high dose of a compound is metabolized to methylmercury, and as it's not a particularly comfortable way to die, it's not worth trying.

@CJDennis - Yes, it is not about mercury in general, but about organic compounds containing it. (I know somebody who ate metallic mercury just for bragging.) Exposure to metallic mercury is over longer time because it vaporizes slowly. I think the problem with fillings is different: The filling is created using a mercury alloy, which is eutectic. That means the amounts of the alloyed metals have a specific relation. If one of the metals is too much, it stays unalloyed as particles in the alloy bulk. If the mixture contained minimally to much mercury, that can diffuse out over long time.

@jamesqf I think your "obvious" relativising comparisons are not warranted. The OP obviously knows more about chemistry then what you are trying to make him look like. Organo-metalic compounds are often extremely poisonous when the metal itself is not and the OP points out exactly that. Take lead and tetraethyllead (gasoline additive) as an example. Methyllead is extremely poisonous and the OP points that out. It should not be dismissed so lightly, if not even offensively, that ethyllead is just something else. It should be explained scientifically.

@CJDennis - To illustrate the toxicity of an organic mercury compound: A scientist doing research specifically about the toxicity of methylmercury died from mercury poisoning. She was clearly aware what she was dealing with. She was protected. Some drops fell on her latex gloves, nothing more. There was no hole, just what went through the gloves by diffusion poisoned her. She died a few month later.

[citation needed]. Did she die from mercury poisoning, or methylmercury poisoning? There are so many compounds made of mercury. Some will be highly toxic, some mildly toxic, and maybe even some not toxic at all.

@CJDennis - It was Karen Wetterhahn, professor of chemistry at Dartmouth College. The toxic substance was dimethylmercury. She died in 1997. See https://sites.dartmouth.edu/dujs/2008/05/16/remembering-karen-wetterhahn/ .

@CJDennis There are actually several referenced cases.  Ceccatelli S, Daré E, Moors M. 2010. Methylmercury-induced neurotoxicity and apoptosis. Chemico-Biological Interactions 188(2): 301-308. doi:10.1016/j.cbi.2010.04.007

@Volker Siegel: Re lower alcohols being toxic, that brings up what seems to be a pretty direct analogy to the relative toxicity of methylmercury and ethylmercury.  Methyl alcohol is quite toxic (https://en.wikipedia.org/wiki/Methanol_toxicity ) while ethyl alcohol is regularly consumed by a large fraction of the human race, and is toxic only in large amounts.  So obviously all alcohols are not equally toxic, so why should we expect all mercury compounds, or lead compounds, to be?

Thiomersal is broken down into two compounds, thiosalicylate and ethylmercury (Ensink 2015).  The thiosalicylate it is relatively non-toxic, and there is even some evidence that this compound could counteract some of the effects of mercury poisoining (Asadi et al 2010), though the mechanism of this inhibition has yet to be elucidated.
Although they have similar names, methylmercury and ethylmercury have very different levels of toxicity.  Methylmercury has long been known to be highly toxic, producing high levels of cell death in the brain, particularly in the cerebellum and the visual cortex (Ceccatelli et al 2010).
Unlike methylmercury, ethylmercury appears unable to cross the blood-brain barrier as fast as it is eliminated in the stool.  Consequently, small quantities of ethylmercury have been shown to be non-toxic, resulting in the relative non-toxicity of thiomersal (Pichichero et al 2002).

Sources:

Asadi S, Zhang B, Weng Z, Angelidou A, Kempuraj D, Alysandratos KD, Theoharides TC. 2010. Luteolin and thiosalicylate inhibit HgCl(2) and thimerosal-induced VEGF release from human mast cells. Int J Immunopathol Pharmacol 23(4): 1015-1020.

Ceccatelli S, Daré E, Moors M. 2010. Methylmercury-induced neurotoxicity and apoptosis. Chemico-Biological Interactions 188(2): 301-308. doi:10.1016/j.cbi.2010.04.007

Ensink E. 2015. Preservative or poison? The science behind Thimerosal. The Substrate (online): http://substrate.asbmb.org/2015/05/15/preservative-or-poison-the-science-behind-thimerosal/

Pichichero ME, Cernichiari E, Lopreiato J, Treanor J. 2002. Mercury concentrations and metabolism in infants receiving vaccines containing thiomersal: a descriptive study. The Lanclet 360(9347): 1737-1741. doi:10.1016/S0140-6736(02)11682-5

is the toxicity of mercury in general primarily focused on its effects in the brain, then?

Primarily; see Ceccatelli et al 2010 if you have access to a library which contains it.

So its still nasty stuff but we simply poop it out fast enough to survive?

@PTwr That really describes a very large number of toxins. Everything has some minimum dose required for it to actually be dangerous, and below that it's usually a case of the body getting rid of it (either through excrement or through some form of decomposition) faster than it can do anything dangerous.

Just as a curiosity - what prevents the body from breaking it down into the more toxic or the two, or one being converted into another (like how Ureic Acid breaking down into ammonia) by the body?

@Pureferret If you examine the structures of thimerosal, ethylmercury and methylmercury, you'll discover that breaking thimerosal down into methylmercury doesn't make sense, structurally; you'll also discover that reactions that turn ethylmercury into methylmercury don't really make sense energetically.

authors: Vladimir F Героям слава


text:
Why is ATP produced in photosynthesis used to synthesize glucose?
In photosynthesis ATP is produced in light-dependent reactions only to go to the Calvin cycle to be turned into glucose to make ATP during respiration:

Why isn't this ATP just directly released into the cell? Is there a benefit to using the ATP to make glucose? Also, ATP can be made in the chloroplasts with cellular respiration? What happens to this ATP?

Okay so i did edit some of the text too, in it's initial form it didnt make sense to most of us, as in the ATP isnt converted to glucose, it's used to catalyze reactions that fix CO₂ into 3-carbon sugars that can result in glucose, bear in mind lipid/nucleic acid metabolism also need these sugars so glucose isnt the only output!

As far as I can understand your question, you wish to know why a plant cell consumes ATP to produce glucose when it can directly use the ATP as an energy molecule.
ATP is an energy currency and is required in different biochemical pathways. However, it is not a good energy storage molecule. Following are the reasons why production of an energy molecule such as glucose is essential:

Not all parts of the plant are photosynthetic. These non-photosynthetic parts need an alternate source of energy. Since ATP is unstable, it cannot be transported to different parts of the plant without degradation.
Since photosynthesis cannot happen in the dark, the plants would require some energy molecule that can be utilized later on, in the dark conditions.
Chloroplasts themselves require ATP in the dark conditions. They express an ATP-ADP translocase that actually imports ATP from the cytosol while pumping out ADP+Pi (See this review).
Plants also need energy storage for seeds. This storage is usually in the form of starch (a polymer of glucose).
Glucose is required for synthesis of cellulose which makes the cell wall of plants.
The glycolytic pathway (including pentose phosphate pathway) produces important metabolites such as ribose (in the form of PRPP, which is important for nucleotide synthesis), pyruvate (which is used to synthesize alanine) etc.
Glucose and some glycolytic metabolites (such as glycerol) also serve as osmolytes i.e. they maintain osmotic pressure in the cell.

Basically, points 4-7 convey that Calvin-Benson cycle not only produces sugar but what it actually does is fix inorganic carbon (as CO2) to organic form (in the form of sugar). So, most (practically all) of the carbon that a photosynthetic plant has, comes from this carbon fixation process and that's how plants are photoautotrophic.

Also NADPH produced should be oxidized to keep constant supply NADP+ for light reaction


text:
How do minute changes in an organism, as a result of evolution, get carried over to next generation
The theory of evolution states that random variations in organisms occur to better suit their surroundings. We take for example a bacteria's flagella. There's a bacteria who has a tube kind of structure that it uses to inject toxins in other cells. Structure of flagella and this tubular structure is very similar. So biologists state that this is clear evidence for evolutionary process wherein this tubular structure underwent gradual changes that resulted into a flagella.
Now my question is, minute changes did occur to this tubular structure, but how do those changes get carried over to the next generation? Almost all components of a cell are created as per the instructions coded into DNA. So does it mean that every minute changes that occur to an organism get recorded into DNA so that they can be carried over? In above example, assume, that a few proteins got accidentally attached to the tubular structure that will help the structure to rotate. Now when this temporarily changed bacteria gets divided into a new one it will have lost that change. So to actually carry over this "beneficial" change would the bacteria have changed its genome? How does this happen? What is the basal mechanism that supports evolutionary changes?

Changes to the organism don't get recorded in the DNA, changes on the DNA generate differences in the organism

As populations expand, generation by generation, they will inevitably
  run into limits on resources. Not all individuals in a population are
  exactly alike as some will have traits that give them an advantage in
  survival. A change in any aspect of the environment can suddenly turn
  what had been just another variation or variant into either an
  advantage or a disadvantage  If a selective pressure (i.e. change in
  the environment), acts against or upon the differences between the
  individuals in a population, you get natural selection, which, through
  time, can cause a population to evolve

http://rmitchellbioanthro.weebly.com/uploads/2/3/7/6/23767919/natselinanutshell.pdf
Evolution consists of two essential things:
Random mutagenesis (in this case a slight change that occurs in the DNA, that causes a slight change in the protein to show up)
The second stage of evolution is natural selection. After the mutagenesis event, nature rigorously selects for the mutation. If the mutation has a fitness cost to the organism, it gets removed (the organism doesn't survive). By removing all things that are more costly than beneficial, nature selects for the fittest.

Take the examples of beetels here (http://evolution.berkeley.edu/evolibrary/article/evo_25)
Very rarely does the external environment directly change the DNA code (you can argue about epigenetics, but that's a different can of worms). Changes in the environment usually dictate the survival of organisms with different traits. In fact what usually happens is a change in the DNA code occurs naturally due to mutagenesis and that change undergoes the rigours of natural selection.
So in you case what might have happened is (I am postulating here, I would recommend a literature search to verify this), your bacteria had a tubular structure that it used to inject toxins in other cells. Some bacteria (due to genetic variation in sexual reproduction) had mutations that allowed it to move this tubular structure. This allowed it to survive more efficiently, and hence reproduce more. Eventually this population of bacteria, slowly replaced the bacteria who had no locomotor control on their "tube", and hence one stage of natural selection has occurred. Now this happens again and again, till the efficiency of the locomotion is optimal.
Might I suggest you read this book ?
Bonner, John Tyler. The evolution of complexity by means of natural selection. Princeton University Press, 1988.

So a fully functional protein can form out of random mutation? Or does that too evolve? Can you give me any links of evidence?

Usually it's due to SNPs and INDELs that you get new versions of proteins.  But again, that's rare where a new protein rises out of nothing.  It's a very iterative process,  and usually the proteins that make the  cut are well conserved from then on.  Usually,  due to genome duplication events,  one gene may code for the protein and the copy will not be under the same selection pressure,  allowing it to accumulate mutations and experiment. Was I able to answer what you were asking?

I'm not a biologist, just have a lot of curiosity in how molecular machinery in cells work. So I have no idea what SNP and INDEL is. Could u tell me the full-form? And I read somewhere that malfunctioning or wrongly folded protein does a lot of harm to cells so will randomly and then successively forming proteins cause problems?

@Shades88 Basically they are small changes in the DNA code. Single Nucleotide Polymorphisms and Insertions Deletions. Anything that causes harm to a cell will cause cell death, and thats the end of that story.

The two other forces of evolution are drift and meiotic drive. Michael Lynch fairly convincingly argues that complexity rarely if at all originates from natural selection.

authors: Александър Блажев

authors: Ангелина Жоголева


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Identify this excreta!
A picture is worth a thousand words!
It's about 1.3cm (1/2") long. We rented a basement and I found this on a machine that was moved in a bit earlier.
I would like to know if there are any mice, rats, etc that could have come in.
We are on the island of Malta, in the Mediterranean sea.
The basement is below a shop that used to sell AC units and the basement was used as a storage. The walls have gaping holes where cables and pipes go in and out, etc. Clearly industrial and not made for the customer to see.

Where are you located? Are you in the city, the country, ...?

I added more details in the post.

I don't think it is possible to identify a species based solely on the length and appearance of its feces

Definitely too big for mice (max 7mm). Could be a rat or a bat (hopefully for you the latter). What was the width? And did you see any clear renmants in the poop? Like beetle shields, hair or plant fibers?

There was nothing around, just that poop and a clean surface around, but this is in a basement we just got. The climate is hot and humid. The only insects we've seen are large cockroaches.

Bat is the other basement creature that comes to mind. It looks like a match as explained in this and several other videos - https://www.youtube.com/watch?v=897Fb9ndids

I just looked at photos of bat poop and they look more bulky, while this one is thin and long.


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Action of tetracycline on 30s ribosomal subunits
My question concerns the mode of action of 30s ribosomal antibiotc inhibitors — tetracyclines. According to some online resources, the antibiotics enter the A-site, which prevents other tRNA from entering the ribosome. Others say that the antibiotic prevents the ribosome from moving along the mRNA. Which one is correct?

Adding references and citations to the "resources" and also naming the particular drug you were interested in would help your chances of getting this question answered considerably.

I am giving the class of antibiotics.  30s ribosomal Inhibitors. Some examples: Aminoglycosides Tetracyclines.

Firstly, as AMR said, you should add the online resources  which you referred to. Secondly, different antibiotics can have different effects. In fact there can be different effects based on concentration. Moreover, it is now established that aminoglycosides are bactericidal because they not just prevent translation but also cause mistranslation leading to toxic products.

Could you expand on "how they prevent" translation.

@RadekMartinez can you first please add references and focus your question on one class of antibiotics such as aminogycosides.

The crystal structure of tetracycline bound to the 30S ribosomal subunit of Thermus thermophilus has been determined by Pioletti et al. and the major binding site (Tet-1) interferes with the location where the A-site tRNA binds as shown in the stereo pair, below:

They write:

“Thus tetracycline can physically prevent the binding of the tRNA to the A-site. This mode of interaction is consistent with the classical model of tetracycline as an inhibitor of A-site occupation, and hence offers a clear explanation of the bacteriostatic effects of tetracycline.”

So the proximal effect would appear to be the first alternative in the question, although the second may be an indirect consequence.


text:
Method of figuring out how much of a certain mRNA is present in a bacterium
I am trying to develop a method for figuring out how much of a certain mRNA is present in a bacterium. This is what I have so far:

Perform a mRNA extraction
Using Electrophoresis, to isolate the wanted mRNA strain (based off of size)

Now, I am not sure how I would quantify the amount of mRNA. I was thinking of using nano drop to test concentration, but I am not sure if that will give a good enough answer. What other methods could I use to quantify the amount of mRNA in my sample?

You should be running qPCR to quantitate how much of a certain mRNA sequence is present in a sample. Remember that there are thousands to tens of thousands of different mRNA sequences present in an RNA prep, not to mention ribosomal RNAs, transfer RNAs, etc. If you then run your RNA prep out on a gel, you're just going to get a smear. Even if you cut out a portion of the gel that corresponds to the expected size of your mRNA of interest, there are going to be lots of other sequences present in that portion as well, so doing a gel purification step then measuring concentration with Nanodrop (which is quite accurate within its working range) won't tell you anything.
Quantitative real-time PCR (qPCR), on the other hand, when run with appropriate controls and standards, can give you a very good idea of approximately how many copies of your sequence of interest there are per nanogram of total RNA.

So I can run qPCR with the standard curve ect... to find the number of mRNA. But how would I isolate the fragment of mRNA I want to test if a gel will not give me good results?


text:
Could I use spiders to catch unwanted insects?
I was wondering if its possible to catch spiders and place them in my greenhouse in order to kill unwanted insect that feast on my plants? I don't really mind presence of spiders since then are not dangerous in my country (Czech republic).
Common species that live outside are Araneus diadematus, we got many that live in presence of human like Tegenaria domestica, but I read that they are type that live at human build constructions and can't really survive outside.

Spiders can definitely be used for pest control along with some beneficial insects, such as ladybugs. Some care should be taken in case the introduced spiders actually cause more harm by, for example, killing ladybugs. An alternative approach is to grow plants that attract beneficial spiders and insects:
https://dengarden.com/gardening/Useful-Insects-For-Plants
https://www.organiclesson.com/beneficial-insects-garden-pest-control/
Perhaps you'll get more info over at gardening.stackexchange.com.

What you describe is called biological pest control. Lacewings and earwigs are more common, but there are ways to use spiders.
http://unossc1.undp.org/GSSDAcademy/SIE/Docs/Vol4/Rearing_spiders.pdf
http://www.annualreviews.org/doi/abs/10.1146/annurev.en.29.010184.001503?journalCode=ento


text:
Antiparallel DNA Strands - Error Correcting Code?
Let me quote Wikipedia.org:
"The two strands of DNA run in opposite directions to each other and are thus antiparallel."
There is a practice or method used for error correction with regard to parking tickets: First the number plate is written down from left to right, then again but in reverse (right to left) order.
So my question is: to what extent does the antiparallelity of both DNA stands constitute an error correcting code?

I can flesh out my answer a bit more if you don't have enough biology background to connect with the info in the linked article

Double-stranded DNA does have redundancy giving a basis for error-correction, but it has nothing to do with the antiparallel nature of the DNA.
Each strand has an orientation, that is the pieces of the backbone are not symmetric and so chemical reactions have to happen in one of the two possible orientations along the strand.  One end of a strand is called the 5' end and the opposite end of the strand is the 3' end.  The two strands of a DNA molecule run in opposite directions (antiparallel), with the 5' end of one strand being adjacent to the 3' end of its partner strand.  The two strands do not contain the same codes in opposite order like your license-plate coding example.
The redundancy is only pair-by-pair.  A nucleotide in one strand is paired with a unique complement nucleotide on the other strand.  It is thus redundant like bit-for-bit odd parity is redundant.  This redundancy allows errors to be detected from a mismatch in what should be a pair, and a damaged nucleotide can be replaced with the correct nucleotide by using the complement of the nucleotide on the other strand.

As you have intuited, complimentary base pairing gives DNA molecules 2-fold redundancy. That is, given the base present on one strand, we can always deduce the base that should be at the corresponding position on the other strand.
Cells take advantage of this redundancy to perform error correction through DNA repair processes. Here is a textbook section that introduces how DNA damage is sensed and how cells can use the complementary base on the other strand to guide repair. It also details how cells can determine which base is "correct" when a mismatched base pair arises during replication.
https://www.ncbi.nlm.nih.gov/books/NBK9900/


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Can any gas other than nitrogen cause decompression sickness (the bends)?
I know that our bodies use most of the oxygen we breathe in during a dive but, wouldn't our tissues, under pressure, absorb more oxygen than we need?  For instance, in normal circumstances, we don't use all the oxygen in each breath and we exhale some (this is what 'rebreathers' are for, right?)
Couldn't any gas we breathe in under pressure cause decompression sickness when we decompress?
Read this, from NASA:

"Astronauts put on their spacesuits several hours before a spacewalk.
The suits are pressurized. This means that the suits are filled with
oxygen.
Once in their suits, astronauts breathe pure oxygen for a few hours.
Breathing only oxygen gets rid of all the nitrogen in an astronaut's
body. If they didn't get rid of the nitrogen, the astronauts might get
gas bubbles in their body when they walked in space. These gas bubbles
can cause astronauts to feel pain in their shoulders, elbows, wrists
and knees. This pain is called getting "the bends" because it affects
the places where the body bends. Scuba divers can also get "the
bends."

Yes, it is possible to get decompression sickness with other gasses, such as the "oxygen bends" or oxygen decompression.  For instance, in this study, they demonstrated that oxygen decompression sickness in mice.  Another study demonstrates a more common non-nitrogen decompression sickness - helium bends.
Undoubtedly you will be wondering at this point why breathing pure oxygen would diminish (or, in certain circumstances, completely remove) the risk of bends as compared with nitrogen.  The reason is simply that oxygen, unlike nitrogen gas, is constantly being metabolized by the body tissues.  Consequently, even if the oxygen levels in your body fluids become elevated, they would have to be way higher than normal levels (like in the first study linked) before you would start to have it accumulating enough to form bubbles.
The body is designed for the shipping and handling of oxygen (think haemoglobin & myoglobin).  Nitrogen, on the other hand, is relatively incidentally present - so long as atmospheric pressure remains relatively constant (which it did until we devised technology allowing us to radically change it), it's present in low levels in all the body tissues without causing any trouble.

Also interesting in this context: https://en.wikipedia.org/wiki/Saturation_diving


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Osmotic pressure
Osmotic pressure is defined as:

The pressure that would have to be applied to a pure solvent to prevent it from passing into a given solution by osmosis.

And yet water moves from low osmotic pressure to high osmotic pressure.
Shouldn't high osmotic pressure prevent osmosis? It would be really helpful is this definition were explained.

In the future please do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). There are good sources of information on this subject including: Wikipedia, and LibreTexts. ——— Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. Thanks!

The definition in your first paragraph doesn't match your understanding in the second. If osmotic pressure is high in "A" relative to "B", you would have to apply a physical pressure to "A" to prevent solvent moving from B to A. If there is no such pressure applied, then solvent does move from B to A. The osmotic pressure and physical pressure are separate and opposite forces.
I prefer to think of osmotic pressure as sort of a "vacuum" that "pulls" solvent towards it (of course it isn't really a vacuum so don't take this analogy too far...). The definition still works given this form of thinking: you'd have to apply as much external pressure to equal the "vacuum" in order to have no movement of solute.

The second paragraph in the question describes two solutions separated by a semipermeable membrane (a membrane that allows water through, but not anything dissolved in the water). As it says, in those conditions, water will move from the section with low osmotic pressure to the solution with high osmotic pressure.
Osmotic pressure, like other colligative properties, is proportional to the concentration of solutes in a solution. So you can think of it is a measure of how much other stuff is in the water. Low osmotic pressure means low solute concentration. High osmotic pressure means high solute concentration. Water moving across a semipermeable membrane from an area of low solute concentration to an area of high solute concentration may be a little more intuitive. Given a barrier to solutes but not water, water will move in a way that will even out the concentration.
Now come back to the definition of osmotic pressure. The definition starts by setting up a very special set of conditions to allow us to measure the pressure -- pure solvent in one compartment, a known concentration in another compartment, and the key difference, pressure to prevent water from moving the way it otherwise would.


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Is there any free software similar to CellDesigner that allows me to represent large networks of biochemical reactions in the human body?
I continually have to review multiple articles, in multiple journals. These articles present how various enzymes, proteins, lipids, carbohydrates, etc. intervene in the processes that lead to certain pathologies (generally neurodegenerative). I have used Celldesigner and Freeplane, but Freeplane is very general software and CellDesigner provides reduced work spaces. I would like to know if there is any other free software that works for this purpose (I usually work in Linux).

Here is a list of such programs. It is an old post but most of the tools it lists appear to still be functional. I found this by just googling "celldesigner alternatives", which is always a good idea to search first for these things.
I have used cytoscape and it is ok, maybe too general also for your purposes. For very simple purposes I have used KEGG pathway in the past, which is in addition to the others.


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Why do you need primers in PCR?
I have read that DNA polymerase requires a primer to bind to the DNA, but I am confused as to why this is the case. When DNA undergoes replication in the cell, there are no primers in the nucleus. Why are they needed in PCR?
Many thanks :)

Who said that there are no primers in the nucleus? Read about Primase. I advise that you pick up a good book on basic molecular biology and read the chapter on replication. Genes by Lewin is a decent book.

@WYSIWYG Thank you for your reply. I see now that there is RNA primase in the nucleus- this makes more sense! However i'm now confused as to why an RNA strand is synthesised? I understand that RNA polymerase works on only one strand and DNA polymerase works on two, however does it not make a difference to the finished product that the ends of the DNA strands are actually RNA?

There is a question about this here. DNA polymerase cannot synthesize without primers but RNA polymerase can. Primase is a kind of RNA polymerase.

Actually, when DNA replicate in cell, there is primer exists. DNA polymerase only can add deoxyribonucleotide (dNTP) to the 3’end of a growing DNA chain, instead of creating a new strand. Here is the picture for DNA replication in legging strand, but is same principal use in leading strand. Primer is synthesized by primase in replication.

It is also worth to mention that, looking at the last step, there is a primer there and must be removed, and DNA maybe shorter in each DNA replication time, and that is why DNA telomere mechanism is proposed. That may be a key point for aging.
So, in PCR, it also needs primers, for DNA polymerase only can only can add dNTP to the 3’end of a growing DNA chain.


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How does the cell cycle affect stem cell fate?
I keep reading about the stages of the cell cycle affecting stem cell fate, however I do not understand how. After all, any cell will have to pass through the whole of the cell cycle, and go through every state.

If you are referring to cells that are differentiated in adults:
Some somatic cells in multi-cellular organisms are post-mitotic, that is, the cells cannot divide, or said in other words, they don't enter in S phase. This cells are said to be in G0 phase, because they keep synthesizing proteins but the won't replicate their DNA.
Another thing we could say about cell cycle having something to do with cell division, is that in G1 and G2 (and , of course in G0) different cell types, produce different proteins. ie: a skeletal muscle cell, produces lots of proteins associated with the contraction, but neurons not so much.
If you are referring to the first cell divisions in a multi-cellular organism's development, then:
in cleavage, the cells are dividing synchronously, and they avoid some cell cycle stages, like g1 or g2 (in cleavage, the cells are just dividing and replicating their DNA; the protein synthesis happens with mRNA inherited from the mother). In this stage, there is no cell growth at all. After some cell divisions, they have to start synthesize mRNA  and, because of that, they start to divide asynchronously. Eventually the cells (for this and also for many other reasons) get differentiated.
I hope this answer is useful :)


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What is this bird of prey?
I recently took a picture of this bird flying around Geneva, Switzerland:

In the beginning, and because it was bright and the subject was against the light, I though it was simply another Buteo buteo as there are many around here. Now by tweaking the brightness and contrast a bit in Lightroom, I can be 99% sure that it is not a Buteo buteo and my mind goes more to a Pernis apivorus, which is another bird of prey present in the region in summertime (May-Sep).
Can anyone tell me if I am correct and what field marks can be deduced from my picture to be sure that it is the right bird?

You can also tell that is an adult male, you can tell it from the very spaced bars on the tail and wings. Beautiful light individual.

Nice photo - Yes, I would agree with you the bands on the tail and the wings suggest that it is a Honey Buzzard Pernis apivorus
http://www.birdwatch.co.uk/categories/articleitem.asp?item=995
http://www.gobirding.eu/Photos/HoneyBuzzard.php

Photo by Dominic Mitchell http://www.birdingetc.com


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Why would a python go after such large prey?
I read that most Pythons would go for smaller prey, around the size of a house cat, but that larger species enjoy crocodiles, deer and even a bit of antelope for dinner. But why?
Now, I realise that evolution is ongoing, and that even in the year infinity evolution can't be expected to result in any subjective measure of "perfection". But, even so, it seems odd to me that this behaviour could have survived the eons.
Perhaps I'm misunderstanding the animal's physiology and it's more mobile in this state than I expect, but isn't this animal utterly defenceless for the next couple of weeks while it digests its tasty snack? Couldn't something else now come along, rip open the snake, steal its crocodile then leave the snake for dead, all without encountering much in the way of effective resistance?
One possible answer I thought of was that other animals may not much like the taste of half-digested crocodile. Conceivably, one could stalk the snake waiting for it to start swallowing the croc, then grab it while the food is still relatively fresh. But I doubt any animal that's not already substantially stronger than the snake would feel too comfortable stalking it in the first place. Is that enough to explain why Pythons have gotten into the habit of apparently making themselves sitting ducks for protracted periods of time rather than simply eating less more often?

I dunno, maybe it is a behaviour liable to be selected out, but it just hasn't happened yet.

Also I may have overestimated the digestion period ("Witnesses said it took this snake about five hours to swallow the crocodile. During that time the snake is vulnerable to attack from a dingo.") based on something I read elsewhere. Anyway, looking forward to your expert thoughtz.

@DonJulian: Not really the sort of deep thought I'm looking for in an answer...


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How does non-homologous end joining (NHEJ) work?
I was reading about non-homologous end joining (NHEJ) in my molecular biology of the gene textbook but the explanation provided in the text was rather vague to me, and I was not able to understand it completely. I understood that NHEJ can be used as a repair mechanism when double-strand breaks in DNA occur. The two broken ends are then joined together. What I didn't understand is how this is done. The two broken ends won't always have complementary bases so, won't this lead to mismatched bases? How is this problem fixed? I really need a detailed explanation of how NHEJ occurs please.

Non-homologous end joining indeed induces errors in the affected sequence. But you have to keep in mind, that NHEJ is an emergency repair mechanism which involves a "repair or die" chance. If the chromosomal break is not repaired it is not unlikely that the cell will get into apoptosis, or, even worse, develops into a cancer cell. Introducing small errors is a relatively small price compared to this, although this can still disrupt genes or regulatory sequences. For the mechanism have a look onto the figure (from the first reference):

For further reading have a look onto the Wikipedia article on NHEJ and/or the following references:

The mechanism of human nonhomologous DNA end joining.
The mechanism of double-strand DNA break repair by the nonhomologous
DNA end-joining pathway.

NHEJ is indeed error prone. It is called "non-homologous" because it does not use a "homologous" template from another sequence-matching piece of DNA to guide the repair. Homologous repairs avoid causing mutations because the similar string of DNA  acts as a template so that the cell knows what letters to put into the gap. When there's no template, there's no way for the repair machinery to know what specific letters to use...hence the mutations in NHEJ.
Interestingly, this NHEJ phenomenon is used to drive the current state-of-the-art in genetic engineering: CRISPR/Cas9 RNA-guided endonucleases. If you cause a double-strand DNA break near the beginning of the protein-coding sequence of a gene, this break will be repaired with NHEJ, causing an "indel" (insertion or deletion) mutation to occur. Inserting or deleting letters into the coding sequence of a gene will cause a "frame shift" where the 3-letter codons which tell the cell which amino acids to use get all jumbled up because the normal 3-3-3-3-3-3-3 pattern is disturbed. In this way, we can turn off genes that we want to target: just cause a frameshift in that gene with CRISPR.
If we want to INSERT something using genome editing, we need "homology directed repair" -- we'll give the CRISPR alongside another string of nucleotides which matches the strings that flank the place we are cutting, with a new sequence in the middle. So when CRISPR makes the cut, our homologous template will stick to the sides of the cut and the center piece will provide the cell with a blueprint for the insertion or edit we want to make.
So, you'll see as you think about it that the "homology" which is missing from NHEJ is the strand used as a repair template, and by manipulating these natural DNA repair processes which may or may not use homologous templates, we have a possible method to turn on, turn off, edit or insert genes. This means NHEJ isn't just a biological process anymore: it is an engineering technique.


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Are all prokaryotic promotor regions the same, or do they differ depending on the product of the transcript?
Are all prokaryotic promotor regions the same or do they differ depending on the protein encoded by the mRNA being transcribed?
What I am thinking is that if activator proteins are a method of transcription regulation, then shouldn't promoter regions differ so that activator proteins have an effect on the  expression of a specific gene?
Please tell me if this is correct, or if I misunderstand something.

Sorry, english is not my first language....

Definitely not. There is a ton of variation from gene to gene, otherwise, as you say, regulation wouldn't work.
That said, the word "promoter" sometimes gets used in different ways. Especially in eukaryotic systems, people will sometimes say "promoter" to mean the entire region upstream of the gene where transcription factors can bind (for yeast, typically within a few hundred base pairs, for mammals, could be many kb away). These regions are extremely variable from gene to gene in all organisms. But for bacteria, the word is more commonly used in a much stricter sense, to mean the region where the polymerase and the associated sigma factor binds -- this is typically one or two very short stretches of DNA (maybe 5-10 base pairs) very precisely located at a specific position from the start of the gene. These regions are much more conserved, but there will still be some variation. Check out http://nar.oxfordjournals.org/content/40/7/2907.full for a very detailed characterization of some of these sequences in E. coli.

This is not my area, but as nobody has answered yet I'll start the ball rolling to try to encourage a more authoratative response.
Long, long ago, before the internet, when I was a post-doc and the emphasis was on bacterial rather than eukaryotic gene expression, I remember hearing something about specific sigma factors differentially controlling initiation of different bacterial genes. A quick internet search brought up something in Wikipedia (section on Specialized sigma factors), a recent review on sigma factors by Chandrangsu et al. (2014), and a more general review of the regulation of bacterial transcription initiation by Browning and Busby(2004).
In general it would appear that you are correct in thinking that promotor regions will differ to some extent, depending on how they are regulated.


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How many protons are pumped out per pair of electrons from NADH in oxidative phosphorylation?
I have searched the web and found that 10 protons are suppose to get pumped out during the electron cycle, but i'm a bit confused.
I'm trying to count, for every complex(1/3/4), the number of protons that are reduced in the matrix versus the number of protons added to the intermembrane space. The numbers don't add up.
my calculations:

complex 1: 4 protons reduced, 4 protons added.
complex 3: 2 protons reduced, 4 protons added.
complex 4: 2 protons reduced(not counting the ones that condens to H2O), 2 protons added.

It seems like the mistake is in complex III. Look at this image from here:

It clearly shows the number of protons reduced in (and taken from) matrix and number of protons pumped into inter-membrane space. So the data becomes:
Complex I:
matrix: 2H+ reduced (from NADH + H+) + 2H+ pumped out
IMS: 4H+ pumped in
Complex II:
matrix: 2H+ reduced (from succinate)
IMS: 0H+ pumped in
Complex III:
matrix: 2H+ pumped out (when not considering complex II, you'd count 4H+ here)
IMS: 4H+ pumped in (2 from complex II)
Complex IV:
matrix: 2H+ reduced (to H2O, we won't consider it as you said) + 2H+ pumped out
IMS: 2H+ pumped in
TOTAL:
matrix: 10H+ subtracted/pumped out (with 2H+ to water, total 12H+)
IMS: 10H+ pumped in
This satisfies your statement that "10 protons are supposed to get pumped out during the electron cycle". I Hope this helps ;)
IMS = inter-membrane space

I just want to add a slight clarifying point to the previous member's already great answer. Keep in mind that these 10 protons that are pumped into the intermembrane space by the end are per one molecule of NADH. So each molecule of NADH will result in 10 protons being transported into the intermembrane space (as previously stated). For each molecule of FADH2, however, only 6 protons are pumped into the intermembrane space. This is because FADH2 skips Complex I (it feeds its electrons to ubiquinone "Q" through Complex II).


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Can a snake deposit venom while drinking?
When a venomous snake drinks, does it deposit even trace amounts of venom into water?
I understand that "drinking" and "biting"(attacking) involve different reflexes and muscle complexes, so it would probably not be "natural" for a snake to deposit venom while drinking, so the question is probably more about the "hermeticity" of the venom sacs/glands - does venom seep out.

Physiologically, venom glands wouldn't normally leak but could be affected by health conditions/age (similar to tissue deterioration seen in older people) but dried venom on the teeth or mouth could be deposited into water during drinking. Dried venom can remain potent for many years: https://phys.org/news/2014-02-snake-venom-decades-potent.html.
Can I ask what led to your question? It's very interesting!


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When does genetic randomization happen?
When two parents (regardless of species) reproduce in sexual reproduction each offspring is generally a random combination of genetic traits from each parent. Their developed traits then depend on the expression of each of their genes per established genetic combinatory science. All well and good.
Now my question - when does the actual randomization of genes for a given offspring happen? Does it happen when the individual sperm and egg cells are formed, or does it happen when they combine?
So does every one of a female's eggs have the same genetics, and every one of a male's sperm have the same genetics, and when the two combine it is randomized to form the zygote?
Or is each egg unique and each sperm unique, and already "pre-randomized", and the combination to form the zygote is then a straight-forward addition?
Or is it some variation or combination of those two options? Maybe the answer actually even differs across species, or across plants vs animals, or fish vs mammals, or something?

Randomization is the act of making random. I have corrected one clear misuse. While an enquiring mind is to be commended, it's owner should learn how to find the answers to its questions himself using the sources available on the internet if he does not have access to a University library. And, indeed, that is what SE Biology expects of posters (see the Help). Google for NCBI Bookshelf, where you can find older editions of standard textbooks in cellular and molecular biology. If these do not answer your question, then post citing the information provided and how it is deficient. Have fun!

Randomisation happens in the forming of the the egg and the sperm. In a first approximation, the egg and the sperm receive a random single chromosome of each of the chromosome pairs during meiosis.
More randomisation happens due to the possibility of crossing over when homologous chromosomes exchange chromosome parts.
EDIT: In terms of the question, bothe the egg and the sperm are pre-randomised.

Your view of the randomization of the parent traits seem a bit wrong and it makes the question a little unclear. But still, I think we can answer it...
The randomization happens at the moment of the creation of sperms and ovules. The two "randomizing processes" are segregation and recombination.


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How can computer predictions of protein folding be verified computationally?
Currently, there is a lot of research focused on solving the folding patterns of proteins using computers (Folding@Home, https://fold.it/portal/, etc.).
The question that I have is: How do you know when you get it right?  Is there some way of verifying, in silico, that you have found a legitimate/correct structure for a protein?

Normally you have an output in silico you'll have to verify by NMR, xray crystallography, or experimentally in other words. If your protein is particularly disordered, however, you must compile many techniques into a conformational ensemble as outlined here. The computational techniques provide lots of data but there's no 100% without experimental verification.

http://biology.stackexchange.com/questions/30240/proteins-folding

@Kendall Although experimental analysis "trumps" modelling, there are methods to analyse the viability of a model (see my answer for more depth).

the best you can do is, modelling using  I-TASSER server or may also prefer Rosetta package, but the question you asked is still a "million dollar question"...

Overview
Modelling has come on leaps and bounds over the last decade or so and in many cases has acted as a sometimes viable, and inexpensive substitute for experimental structures.

How do you know when you get it right?

Ultimately, one still needs experimental evidence to know when a model generated in silico is right. But there are ways of scoring a model for how likely it is to be right.

Is there some way of verifying, in silico, that you have found a legitimate/correct structure for a protein?

There are lots of ways to score and verify your models. Each method tells you something slightly different about the merits, or lack thereof, of your structural model. Some are designed to weed out the obviously awful models and some allow you to detect exactly where your model looks to be accurate or inaccurate.
MODELLER Homology modelling output verification on the fly.
I am most familiar with modeller for homology modelling. Other softwares are available and they are each evaluated by CASP every two years since 1994.
In homology modelling there are 3 common scoring systems that can be used to assess the biochemical viability of a model. This email covers when to use each one. My answer expands and explains a bit more.
molpdf is the Modeller objective function.
GA341, discussed here is derived from  Z-score (calculated with a statistical potential
function), which is a target-template sequence identity, and a
measure of structural compactness.
DOPE is a more up to date method, first published in 2006, and is more true to "biological viability". From the publication:

DOPE is based on an improved reference
  state that corresponds to noninteracting atoms in a homogeneous sphere with the radius dependent on
  a sample native structure; it thus accounts for the finite and spherical shape of the native structures.

Which to use depends on what you want to do with the model, but of those three scores, DOPE is the most reliable at separating native-like models from "decoys".  DOPE is usually the starting place for figuring out which models might be right and which models are just plain rubbish.
Note:  If you use Rosetta then there will be equivalents to these, or you can run your generated models through these techniques. If you are using SWISS MODEL that comes with it's own somewhat black box verification techniques but you can still export the model for further verification.
General model check against experimental data.
A further validation of homology modelling methods or other structural models is ProSA. ProSA provides a great visual representation of where the z-score lies amongst actual crystal and NMR structures. There are probably others that do similar functions, but this is my personal go-to to get an idea of where my structure lies among experimentally gathered structures.
Sensitive residue by residue verification.
Although the aforementioned methods examine each residue, they usually output an overall score. Residue by residue scores are also available and require a lot of careful interpretation. For example, if you are analysing catalytic activity, a surface looping region that scores poorly might not be an issue, but a core catalytic residue that scores poorly renders the model useless. This means that just because your model has a good (lower) overall DOPE score than another model, doesn't mean it is necessarily a more accurate model for what you are interested in.
There are plenty of sensitive modelling scoring systems. Some of which are XdVal, MTZdump, the famous albeit old-school Ramachandran Plotting method, pdbU, pdbSNAFU, PROCHECK, Verify3D, and ERRAT to name a few. Each has a place when checking how correct your model is.

Thanks, this is very informative.  I was always wondering if there was some kind of "magic formula" which told you that your folding was correct.  I'll take a better look at specifics of those models, but this now leads me to wonder how Folding@Home and others manage to "solve" protein structures.

At this point, it must be verified experimentally.
In this foldit research paper, they use software and user input to design essentially an enhanced version of a naturally occurring protein, but they then physically make their new protein and determine its structure experimentally, using x-ray crystallography. Overall, they use a lot of trial and error
http://homes.cs.washington.edu/~zoran/foldit-nbt-2012.pdf
Projects like this are kind of geared towards towards the goal of being able to determine a protein's structure from its amino acid sequence in silico. Once we achieve this ability, it will be revolutionary. However it is very difficult, because making such predictions accurately would require the use of quantum mechanics in a way that is extremely difficult to computationally model. These projects use shortcuts to get around this problem, so their results aren't very accurate, but they can be accurate enough to be useful, as shown in that paper.

Here you are discussing ab initio modelling which is complex as you state. However, "in silico" modelling also includes homology structural modelling, something you miss out entirely from the answer. Homology modelling is a much more established method and has been shown to be very accurate in many circumstances. The key is that structural information from similar known structures can aid the prediction. ab initio is only used in some rare instances if homology modelling cannot be used and experimental analysis is not available.