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Does any animal species have two sexes and more genders?
Are there any animal species that have two sexes and a kind of different internal diversification in two genders or more? I don't mean something like different-task-based diversity, but something biological?
For example let's imagine a species with:

2 sexes (male and female)
2 gender (A and B)

and individuals can match iff they are not only of different sex but also of different gender.
So you can only have Ma-Fb, Mb-Fa.

What sort of other classification are you thinking of? There are lots of different classifications, e.g. both male and female humans can have any of the four blood groups. Another example could be dogs (or a lot of other animal species) where another classification is race - each race has male and female dogs.

I would exclude those features because they don't determine directly the matching process (dogs don't match iff they are of different races, human beings don't if they are of different blood group). I've in mind some kind of upper-level biological feature, like sex is (different apparatus), that can influence sexual-selection.

You might find some things of interest with the search term 'alternative reproductive tactics'.

Your definition isn't very good. For instance, a monolingual German speaker and a monolingual French speaker are extremely unlikely to "mate" in a conventional reality (in fact, there is even evidence somewhat supporting this). Obviously it's preposterous to call them "different genders", however.

related: http://biology.stackexchange.com/questions/2738/why-do-only-only-two-sexes-exist-for-animals

The question is interesting but I think there is an issue of definition. Different sex necessarily imply different gender (the opposite is not true though).  Strictly speaking, any standard sexual species would fit your description. A woman can only mate with a man if they are of different gender (because they necessarily are of different gender given that they are of different sex). What you meant is rather something like: 2 sex and 4 genders (including the sexes).

I find this very unclear. Are you talking about specifically about gender (which can be hard to apply for non-human animals) or any kind of trait that can affect mating success and work as some sort of "mating type"?

@Remi.b That depends on you definition of gender. A fairly common definition is to see gender as a social construct (gender identity), which means that different sexes doesn't necessarily imply different genders.

@fileunderwater You're right!

Many organisms have multiple sexes. For instance, here is one which apparently has 7 (and each sex, or "mating type" can only mate with the others). The "gotcha" is that, mostly, they're unicellular organisms where mating in itself is weird to begin with. I haven't ever heard of a metazoan which truly has more than one sex (there may be variation within the males or females, but I think the sperms or eggs are always interchangeable).
Gender, I think, is more of a social term relevant to human behavior. Especially nowadays, so much of the literature and understanding of what is referred to as "gender" is closely linked to things such as gender identity, sexuality, gender roles and personality that is difficult to see how you could meaningfully speak about the "gender" of (non-human) animals.
It's analogous to the idea of "animal language" - certainly some animals may be said to behave in stereotypical ways which influence their mating behavior. Does that mean that what is written about human gender applies? I suspect precious little of it would. I would be quite skeptical of someone discussing gender (in the modern sense) for even uncivilized humans, let alone non-human animals.

Yes, it is called Alternative Mating Strategies and is well known. As an example High-backed pygmy swordtail (a fish) are known for having two types of males, one that is large and aggressive and another that is small and looks like a female to avoid aggression from other males.

There are hermaphrodites and gender changing (M->F, F->M) fish.  Also occasionally, there are also individuals who are neither male nor female, which may or may not count here.
However, I haven't seen 3+ separate genders except for fungi, which might occasionally be multicellular, but probably not what you are thinking of. Fungal genders are so many because they define combinations where mating is compatible.  This news story has a decent summary of why as far as gametes goes, larger animals are known to have only 2 gametic genders, while fungi can have thousands.  You might say that bacteria have gender when they want it (when they have a pili-containing plasmid) and otherwise they have none - any individual may transfer DNA to another under the right conditions (like death).
I know this isn't what you are asking about, but this is the closest I can find. Digging around, biologist Joan Roughgarden has written a book "Evolution's Rainbow" about cases where there may be more than one social role in a given species for biologically male or females - dominance, display, homosexuality and behaviors like this.  Social gender roles has been a way of talking about the biological nature of human social roles since the 1970s - see also Sarah Hrdy.

You're right when you say that social gender is the closest notion to what I might be looking for. A question: can a social gender of a certain individual change over time? If yes, I would exclude it from my research because I'm looking of something can't change naturally over time, as sex does.

I really believe the social gender can change over time - I think if you look around you will find lots of human examples.  Its harder to decide for animals but I'd be surprised there were no supporting cases to be found.  Animals including humans have this wonderful but slippery quality when it comes to their personality/identity - they can learn and change.  Large changes in social environment can usually change us all a lot. For people you should look at the Big Five personality tests - might give you some ideas?

Are there any computational model of sexual reproduction?

too many to count.  from cell division to population models.  ask a question, but maybe think about what sort of model you'd like.  pop = pop * 3.5 - deaths; is a population model.

The closest thing you will find to what you're looking for, I think, are animals with multiple different mating strategies where one sex (usually the male) can have multiple distinct phenotypes. Some examples include:
Patas monkeys, where some males are large and have harems of females while others are dubbed "sneak maters" and instead of having their own harem they sneak in and mate with females in another male's harem
Scarab beetles, where males either have a horn or lack one. Horned males defend their females at their tunnel entrances while hornless males sneak into tunnels to mate with females

(I also remember reading about this one species of waterfowl that had three distinct male phenotypes, but I can't remember the name off the top of my head, so if anyone else knows what I'm thinking of go ahead and comment)

I'm not sure what you mean by "gender" in the context of non-human organisms.  Gender is usually defined as the intersection between biologically determined sex, and the surrounding culture.
Maybe you could argue that in social insects like, say, ants, the fertile queen and the infertile female workers diverge so much in behavior and gene expression that they aren't the same "sex", or that they could be considered different "genders", but I  think that is really stretching the usual definitions of those terms.

Tetrahymena thermophila is an organism with 7 different "fuzzy" genders, not only male and female. Its seven sexes are rather prosaically named I, II, III, IV, V, VI and VII. An individual of a given sex can mate with individuals of any except its own, so there are 21 possible orientations. Here is the link: Zoologger: The hairy beast with seven fuzzy sexes

The white-throated sparrow has two sexes (male or female), but also has an addition "gender" (tan or stripe).
So male will only mate with female. AND Tan will only mate with Stripe
This behavior is probably due to a massive chromosome inversion of 1100 genes on chromosome 2. It is starting to cause the birds to act as if it were a second sex chromosome.
http://www.nature.com/news/the-sparrow-with-four-sexes-1.21018

The males of some Lake Tanganika cichlid species such as Lamprologus callipterus exhibit extreme dimorphism of behaviour and size (see e.g. https://www.jstor.org/stable/40407772). These represent alternative reproductive strategies for mating with the same female population though; the big aggressive 'nest males' attempt to guard a 'harem', while the small 'dwarf males' attempt to sneak in, exploiting the fact that they look similar to females and can sometimes deceive the nest males.
I'm not sure this is completely answers your question though. The assortative "Ma-Fb, Mb-Fa" example you give almost certainly does not occur (at least for long) since that would result in two reproductively isolated populations which would speciate rapidly.


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Accessing Expression Levels for Genes of Interest from GEO Experiments
I have a list of 100 lncRNAs (long non-coding RNAs). For each of these RNAs, I would like to query GEO to find any experiments that used a high throughput sequencing platform and detected expression levels of that RNA in FPKM. To filter further, I'd like to have those expression levels found in controls only. The last filter is to find experiments which found the specific RNA's expression in smooth muscle tissue.
Here are some example lncRNAs:

CDC37L1-AS1
LCMT1-AS1
FLJ21408
CDIPT-AS1
LINC00920
TAT-AS1
SUZ12P1

Is there any way to do any of this? Any help would be appreciated.
Thanks.

You cannot query GEO or SRA using the gene names that are present in an expression data. You have to manually do this. Or you can download selected datasets. Otherwise, as Maxim has pointed out, you should refer to papers/databases that have collected information from different datasets.

You could look at supplementary and methods section of "The Landscape of Long Noncoding RNAs in the Human Transcriptome" paper. They've collected RNASeq samples from TCGA, ENCODE and MCTP and processed it with their pipeline (most of it are filtering and GSEA) to detect novel lncRNAs and associate them with cancer pathogenesis. Their statistics, processing and cross-validation look clean and accurate.
To extract signatures from GEO, you could use GEO2Enrichr. Then calculate the differential expression of tissue-specific libraries in Enrichr. Also, you could submit gene list to Enrichr's Crowd libraries and find GEO entries with a reasonable number of mapped genes first.

That paper had some great baseline FPKMs of interest. Using R, I was able to grab their data and work with it nicely. Thanks for the help.

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Trees ability to transport water
How can trees be able to transport hundreds of liters of water all the way up to the crown and out in the leaves?

This question places much emphasis on quantity, I vote to leave open.

The most popular theory is the ‘hydraulic limitation hypothesis’ (Ryan & Yoder, 1997), which suggests that as trees grow taller, it becomes more difficult to supply water to their leaves. This hydraulic limitation results in reduced transpiration and less photo-synthesis, causing reduced growth.
It is known that in larger/taller trees water supply is limited by two factors — distance and gravity. Larger trees have a longer pathway of transporting tissue, this tissue is known as xylem. This is known as hydraulic resistance and makes it more strenuous for the water to move around in the tree. So now not only is the pathway long, but the water also has to beat gravity. Increased force is necessary to pull the water up to the highest leaves. Additional difficulty comes from the trees growing upright. Fast - growing/short trees frequently have shorter life-spans. They achieve their expeditious growth by having broader, wider xylem vessels, this increasing their hydraulic efficiency. At the same time this provides space for embolisms. An embolism makes it unable for a xylem vessel to transport water. Taller, slow-growing trees are longer-lived, this is caused by them having multiple xylem vessels, rather than having only a few wider ones like the fast-growing trees. Short-growing trees also have a more secured hydraulic system, preventing the forming of air-locks.

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Large set of semen microscope images needed
As a course project I have to write an algorithm whose purpose is to analyze a sperm sample (total number, motility etc). In order to do that though, I need to have a sufficient number of images to use during the coding and testing parts.
Do you know if there is any dataset available with semen images? It would also help if the corresponding stats of the images are also given, so that I can use them as a benchmark to see how well my algorithm works.
Thanks in advance

Researchers, male anyway, have tended to collect their own samples.

Yes, check out the methods for library construction used by one of the authors in this classic paper: http://hogness.stanford.edu/PDFs/62_isolation_and_nucleotide.pdf

@AMR Yeah, that's a pretty bright idea..
go ahead and jerk off every single day of the week...

I wasn't kidding. That is actually what researchers in human sperm do. mdperry gave you a paper where the first author was the source shown in the methods. I have also seen a researcher mention it in a documentary on fertility. And I know of a lecturer who gets one of her male students to provide the lab techs with a fresh sample for her lecture on gametogenesis a few hours before. They set up a microscope with a video camera and project it onto a screen in the lecture hall. It is really quite amazing. This is science and sometimes scientists have to be their own test subjects.

Also if you want to be taken seriously as a Biologist, you need to learn to use terms such as "Collect a Sample" in place of "jerk off." The Biologists in the room will know what you mean without needing to be indelicate. If you must refer to the method of sample collection, then masturbation is the more appropriate terminology.


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

Have you read this quite good article? What don't you understand after reading it?

@MattDMo well, wikipedia articles are always explanatory, but in this case, I can't spot any part that refers to weather dust-mite allergy or allergies in general are inherent or not..

Allergies are caused by one's immune system.  If you had never been exposed to the allergen, you would not experience any symptoms.  So they are not innate or inherent.
Why do people develop food allergies after repeated exposure?  I have not read any convincing explanations for the biology behind this.  When you look at the heavy-chain switching that takes place in B-cells, the IgE that are responsible for allergy symptoms are the terminal switch, so those antibody variable regions have already been selected during your life history up until that point.


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Blood sampling at home
I want to collect small blood samples at regular intervals (e.g. every 8 hours or more often) over a longer period (weeks to months). To avoid having to go to a lab or doctor to have this done, I want to do it at home. I will need to extract mRNA from PBMC from the samples.
Assume a test tube in which you have a piece of filtration paper. You prick your finger and let a couple of drops of blood soak into the filtration paper, and then seal the sample in the tube, and immediately place it in your regular freezer.
How long will the mRNA survive under these conditions?
Will it be better just to let the sample dry out inside the tube (e.g. using a desscant), or store it at room temperature?
Will it be possible to store it for e.g. a week before sending the batch in for analysis?


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What is the chemical makeup of mealworm frass?
We have been raising mealworms for some time and while mealworm frass has proven very useful as a plant fertilizer, I started wondering about other potential uses of this leftover waste.
Can someone please explain what kind of compounds make up the frass from mealworms as percentages of overall makeup?
In particular I would like to understand how mealworm waste compares to other commonly used animal wastes used as fertilizer.
Bonus points if you can suggest other applications (than just fertilizer) for mealworm frass!


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The Ancient Kingdom of Monera
Why exactly were bacteria and archaea kingdoms separated from the now unused kingdom of Monera? Aren't they the same? They are both prokaryotes, so what is the difference?

I'm surprised this term shows up much anymore. Though it's a part of history now, the following paper by Woese demonstrated the three domain system long ago.
This, however, is the net result of the sequenced genomes of eukaryotes, archaea and bacteria:

Source: Toward automatic reconstruction of a highly resolved tree of life.
The phylogenetic differences between these organisms shed light that bacteria and archaebacteria were not as closely related as was initially though, hence the abolishment of Monera.

As you note, "Monera" includes both Bacteria and Archaea -- but genetic analysis and molecular comparisons reveal without a shadow of a doubt that Archaea share a more recent common ancestor with Eukaryota than they do with Bacteria. Consequently, "Monera" is a paraphyletic group, not a proper taxonomic category.  Thus the term has been abandoned in favor of the three domain model.
Edit You'll find quite a nice explanation of this at the Wikipedia page for Monera.
While modern evolutionary biology textbooks tend not to discuss the now outdated term "Monera", each of the following textbooks lays out the relation among the three domains and discusses the reasons that we avoid paraphyletic groups: Futuyma Evolution 2nd Edition, Herron and Freeman Evolutionary Analysis 5th edition, Bergstrom and Dugatkin Evolution 1st Edition, Zimmer and Emlen Evolution 1st edition, Barton et al Evolution 1st Edition. (Presumably other texts and other editions would cover the same ground).

Can you substantiate with some references ?

Any basic biology textbook will explain the relationship among Bacteria, Archaea, and Eukaryota. Any evolutionary biology textbook will describe the problems with paraphyletic groups. But you don't have to go that far afield. The second paragraph of the wikipedia entry on Monera lays out pretty much what I've written above: with links to explain the three kingdom system and the problem with paraphyletic groups: http://en.wikipedia.org/wiki/Monera

If you know this much then please edit your answer and put appropriate references to it. Answers with out proper references are not welcomed even if you are 100% sure.

A question: is the wikipedia an appropriate reference? The advantage is that it is so easy to access directly from here: no books to request, etc., etc.

Wikipedia is an easily accessible free encyclopedia..OK.. you can use it as a reference or you can name the book you have referenced with the author's name. Am I clear ?

Could the down-voter explain what is wrong with my answer?


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How long does it take to extract a tree core for dendrochronological analysis
I'm going to do research in the tropics and am considering using tree cores for part of my analysis. However, for my planning:
How long does it take on average to extract a tree core of a tree with dbh ~50 cm? Trees will vary in wood density between 0.2 and 0.8.
The time includes labelling and storing in a bag, etc.
Tools: increment haglof borer. So I won't take a whole cross section, rather a small core of ~5 mm diameter that goes until the core.
And no picture because I need a more high quality image to be able to do my analysis.

Extract the core?  What do you mean?  Do you mean cut a cross-section?  In any case, it will very much depend what tools you have, how fast you work, etc.

You want to store cross section of 50cm tree cross-section in a bag? Can't you just take pictures?

Oh I guess you're planning to drill a sample through the trunk, are you?

Exactly, that is the plan.

Given the assumption that you know how to properly core (i.e., you've done this before): taking into account fatigue, bark abnormalities, post-processing and storage, and walking between nearby trees, I'd guess you'd average 5-10 every hour across the course of a full day.

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Relationship between food decay and electric current
I am planning to do a little experiment on investigating the relationship between food (organic) decay and the electric current.
I am going to place the food (ex.banana) on top of an aluminum foil, then hook the foil to a battery.

However, this doesn't seem convincing that it's going to work.
Is there any better way to experiment this?

I'm not sure if this falls under "biology" category
Also, it doesn't have to be banana, it could be avocado, lettuce, apple etc.
Thank you

What do you expect will happen?

I expect that food decay will slow down since the current might zap the bacterias @bpedit

Nice drawing of the experiment. However, I do not expect you will find anything. As a reference: electroporation is an extremely common method used in laboratories, many bacterial cells survive, and a pulse of ~12500 V/cm is used. Please don't try this at home, because I expect already a fraction of this pulse will lead to exploding bananas.

Bananas, unless you like mush, become inedible long before any bacterial decay. The brown spots and softening that occur are due to ripening  processes in the banana. Some of the amino acids in the banana are metabolized to produce ethylene. As with other fruits, ethylene acts as a hormone to accelerate the conversion of starches to sugars. The banana gets sweeter while at the same time getting musher. http://www.livestrong.com/article/466183-is-eating-a-banana-with-brown-spots-bad-for-you/
As far as your experimental design, you would need to stick electrodes into the banana to attempt to run a current through it. But I doubt this will work because, to conduct the current inside the banana, there needs to be a certain amount of water, free ions and the structure to allow the ions to move. In my opinion, bananas have too little moisture content for this to occur.
Aiming to affect bacteria on the surface of the banana might be a doable experiment. But the methods that come to my mind involve immersing the banana in an electrolytic solution possibly leading to un-yumminess and not at all guaranteed to work.


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A way to measure ripeness of a fruit
I'm doing an experiment how fast fruits ripen and decay
I'm wondering how to measure the ripeness of a fruit(banana, mango, tomato, kiwi etc.) so that I will get a quantitative results.
I have looked at using penetrometer to see how squishy it is. Is there any other ways to do it?
If not, I'm thinking of getting qualitative results. Is there any tips of making good qualitative results?
thanks

Sorry, I am not sure if this falls into Biology category

I suspect the answers will depend greatly on which fruit(s) you are considering measuring.

At what stage of development will you be observing the fruits? Are they going to be fruits from the supermarket, or do you have access to the trees?

Just a fruit from the supermarket

Asides from just eyeballing the change in color/consistency, Wikipedia suggests using iodine for a qualitative measurement (though without reference):

Iodine (I) can be used to determine whether fruit is ripening or rotting by showing whether the starch in the fruit has turned into sugar. For example, a drop of iodine on a slightly rotten part (not the skin) of an apple will stay yellow or orange, since starch is no longer present. If the iodine is applied and takes 2–3 seconds to turn dark blue or black, then the process of ripening has begun but is not yet complete. If the iodine becomes black immediately, then most of the starch is still present at high concentrations in the sample, and hence the fruit hasn't fully started to ripen.

A quantitative method applicable to many kinds of fruit is going to be tricky. If you have a spectrophotometer you could measure the changes in light absorption as the fruit ages. You will probably want to measure the absorptions of control fruits as they age and then compare them to fruits from whatever experiment you perform.
Another possibility is measuring ethylene and/or carbon dioxide production. As fruits ripen they produce more of both these gasses, but this increase does not follow a neat linear correlation with time to put it lightly. Non-climacteric fruits, if you use them, may also be problematic here as they do not show such increase in gas production.

Merzlyak, M. N., Gitelson, A. A., Chivkunova, O. B., & Rakitin, V.
Y.    (1999). Non‐destructive optical detection of pigment changes
during    leaf senescence and fruit ripening. Physiologia plantarum,
106(1),    135-141.
Burg, S. P., & Burg, E. A. (1962). Role of ethylene in fruit
ripening. Plant Physiology, 37(2), 179.


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How does the color of henna fade?
Henna contain lawsone pigment that attaches to the proteins of the skin,hair,etc.But after a few weeks the color fades?
How does the color fade?
Is the pigment volatile or it is degraded by the body?

It doesn't become volatile nor is it degraded. Neither is really possible because the dye (lawsone) forms very strong bonds with protein molecules and also penetrates the skin quite well [source: here].
Henna fades with time via exfoliation. In other words, it fades progressively as additional layers of skin die and fall (or "slough") off.

Is the same for hair and nails

almost certainly....


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Treatment of cancer
In treatment of cancer, radiation is given, but radiation can also be the cause of cancer. In the drugs of chemotherapy it is written that it is highly carcinogenic. Then why are such methods performed? Is there any recently discovered new method to cure cancer?

It is clearly a trade-off between benefit and harm. Often cancers which are irradiated are the ones, that cannot be removed surgically (or completely). Then the tumor is immediately dangerous for the patient. From the dose the patient gets, you can calculate how likely additional damage is. And then you need to make a decision.
The same is true for the "classic" chemotherapeutic drugs (like Paclitaxel or Carboplatin), which attack all dividing cells. They have a lot of side-effects, but again, there is a trade-off between the benefit this drug has and the harm it causes. See references 1 and 2 for some more details.
There are quite a few new therapy options besides the "classic" ones. These include oncolytic viruses aimed against the tumor (see reference 3), as well as targeted therapies (see reference 4) which only attack certain molecules or proteins important for the cancer. And last, but not least the probably most important new therapy option are immunotherapies to turn the immune system against the tumor. This gives (when the patient is susceptible), spectacular results and I think there will be a lot of development in this field in the future. See reference 5 for details.
An overview over the new therapy options can be found in reference 6.
References:

Long term side effects of brain tumour radiotherapy
Therapy-Related Secondary Cancers
Oncolytic viruses: a new class of immunotherapy drugs
Targeted Cancer Therapies
Immunotherapy: Using the Immune System to Treat Cancer
Overview of Targeted Therapies for Cancer


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How is output of DNA assembler measured?
I developed own DNA assembly pipeline. Input is set of reads and output is set of contigs.
Many papers measure own algorithms and compare it against each other. There are basic metrics like:

N50, N70..,
number of contigs,
genom coverage,
error rate

I download tool QUAST and there I can see metric N50, L50, where is easy to develop own computation. But how I can measure error rate of my output contigs? Is there any tool which can do it?
I searched in many papers but I cannot find way how they do it. I would like to compare with some assemblers with some general way. I found only hints that it should be done by aligning contigs to reference genomes but I do not know how and if it is right way.

This is just data parsing. You can use simple scripts for this.

Can you please describe more, or some example?

If you are interested on the topic of how to compare assemblers, have a look at assemblathon. That group has two papers and working on a third about comparing genome assembly algorithms.


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why dna polymerase 3 requires a primer for replication
Why DNA polymerase 3 needs a primer to star replication.And whats happens when there is no AUG sequence on entire DNA.

You are confused among DNA replication, DNA transcrption, and RNA translation.
First, DNA replication happens during cell division, it create two exactly same daughter DNA.
Second, DNA transcription transcribes DNA sequence into RNA sequence, this RNA sequence may be used to synthesize protein, or RNA itself as signal, etc.
Third, RNA translation is the RNA sequence (codon) recognized by tRNA, and then synthesize protein sequence.
AUG is a codon in the RNA, the is recognized by tRNA, and then start translation. And please remember, DNA use A, G, C, T, but RNA use A, G, C, U, there is no U in DNA.
For DNA synthesis, why does it need primer? I have another answer for solving your question: https://biology.stackexchange.com/a/40954/17473


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Why are vegetables either red or yellow?
Have you ever wondered why these two colors occur so often? Take these:
onion
waltnut
potato
carrot/parsley
and even cabbage which can be green or red.
Why these two pigments? Or is it just one pigment and it's just its concentration that makes the difference?
Thanks for any explanations!

As many plants do, many of vegetable do photosynthesis. For photosynthesis, chlorophylls, which are green, and carotenes, which are yellow to red, play important roles. When chlorophylls get less, you might see yellow to red color due to carotene. When chlorophylls are degraded, they get light brown. In some vegitable, such as tomatoes, lycopene, which is an intermediate of carotene synthesis, is accumulated.
https://en.wikipedia.org/wiki/Lycopene
Another popular pigment is anthocyanin, the color of which is red to purple. Various functions of anthocyanin are suggested from sun-shade, to an antioxidant, to attracting birds in fruits.
https://en.wikipedia.org/wiki/Anthocyanin

A lot of fruit and veg are green when unripe and become brightly coloured when they are ready to eat (obviously not true for all, but most fruit/veg does).
This is probably deliberate as a mechanism to signal to birds and animals that it is ready to eat, so that they can disperse the seeds inside.
Red and Yellow are bright colours not usually seen on plants except of fruit/veg, and flowers (which are brightly coloured to attract bees and whatnot), so it makes sense these could be used as signals.
http://www.rosincerate.com/2015/07/colour-changing-fruits-and-veggies.html


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What is the difference between the Modern Synthesis and the Extended Synthesis?
The NCBI talks about "Evolution beyond neo-Darwinism: a new conceptual framework." (source).
What is the difference between the Modern Synthesis and the Extended Synthesis?

The term Extended Synthesis has been invented very recently and the concept was defended in these two papers

Laland et al. 2014
Laland et al. 2015

I read each paper when it came out and haven't reread them since. Here is a short summary of what I remember.
Those who want to use term Extended Synthesis
In short, they are arguing new findings have extended our understanding of evolutionary biology so much so that we should rename our theory of evolution. The main findings they are talking about concern the field of evo-devo (merging Evolutionary biology and Developmental biology). The subjects that they consider having radically advanced our understanding of evolutionary biology include niche construction and inheritance of niche, developmental bias, plasticity, cultural evolution and epigenetics.
Those who do not want to use term Extended Synthesis
We have discussed both papers in groups in my department and in short, we pretty much all ended up saying that:
It is true that our understanding of evolutionary processes have advanced a lot since the time of Wright, Fisher, Muller, Kimura, and others. However...

There is no important enough rethinking that deserves a renaming of our Theory of Evolution
Most arguments are based on rephrasing of old concept without bringing anything new. This is especially obvious when reading the 2015 paper.
Do we really care about this debate anyway? It is just a name!

Reading
I recommend reading the 2014 paper as 1) offer both point of views and 2) is pretty short.
Note
I do not know your level of knowledge in evolutionary biology but it might be a pretty bad idea to start with complicated subjects such as evo-devo, niche construction, epigenetics, developmental bias, etc...

As far as I know, Neo-Darwinian mechanisms rely heavily on Darwin's proposed evolutionary mechanisms plus the Mendellian genetics but both were insufficient and even contrary to scientific data. On the other hand, the Extended Synthesis is supported by scientific data. In fact, those who hold onto the Extended Synthesis can explain how organisms evolve (empirically than theoretically) than either Darwin or Neo-Darwinists can.

Yes the basis of what we called neo-darwinism or the Modern synthesis of Evolution is pretty much merging the work of Darwin and Mendel. This work of the early 21th century was heavily supported by evidence (where di you read the opposite?). A lot of work has been done since then and our knowledge have gradually improved. When referring to the Modern synthesis we usually include today's knowledge and not only the knowledge we had in the 1940s.


text:
Chitin, homo or heteropolysaccharide?
My teacher told me that Chitin is a heteropolysaccharide but my book regards it as a homopolysaccharide.I am so confused

Even teachers are sometimes wrong. ;)
Chitin is a homopolysaccharide. This just means that it is made up of repeating units of the same monosaccharide - in this case that monosaccharide is N-acetylglucosamine. Other examples of homopolysaccharides are glycogen and cellulose.
The basic structure of chitin is shown below as a polymer of two N-acetylglucosamine units:

Homopolysaccharides can be linear chains or branched, as long as they are made up of just one type of sugar unit. A heteropolysaccharide is made up of multiple different monosaccharide units. Glycosaminoglycans would be an example of a heterpolysaccharide as they contain two different sugar units.


text:
Microbiology- Pseudomonas aeruginosa, BSAC data
I tested Pseudomonas aeruginosaagainst various antibiotics, using Stokes and Kirby-Bauer. When I compared my results with BSAC data it was completely different (understandable) but why for a lot of the antibiotics did BSAC state 'no information available'?


text:
Are there human-ingestible liquids that do not contain water?
My son asked me a question that stumped me: Is there anything a human can drink that does not contain water?
It stemmed from a conversation in beverages in general where I was pointing out that they all are based on water...coffee, soda, milk, etc.
That's when he asked if there are any beverages that don't contain water. Given that nearly all of the water and even solid food I could think of contains water, I couldn't come up with anything, but now I'm curious about it to so came here to ask the experts!

Ethanol, glycerol, plant and animal oils/fats (triglycerides), etc. This link might help: https://www.reddit.com/r/askscience/comments/2nbs8p/can_humans_safely_drink_any_liquid_besides_water/ Great question by the way.

Forgot to add deuterium to that list. Just a disclaimer, obviously none of those could be a substitute for water, but you could definitely drink them ;)

@CDB - Deuterium is a hydrogen isotope. Hydrogen is not a fluid under normal earthly conditions. Further, EtOH always contains traces of water. The glycerine alternative and other oils, however, are a very nice example I guess. Worthy of an answer?

@Christiaan - Apologies, my bad. I meant deuterium oxide, which is actually, however much I hesitate to call it, a form of water. Still not really water though, seeing as it is 2H2O, so I thought it would fit in nicely on that list. Thank you for catching that and I apologize for the confusion.

@CDB - no need for apologies! However, water containing deuterium (D) is still water, just heavier. Water is water from a chemical point of view, so I disagree with your notion that DHO or D2O isn't water.

@Christiaan - From a chemical point of view, I completely agree with you. However, from a biological point of view, seeing as it cannot be used quite like water, I see it as more of a water variant, therefore I thought the OP might be interested.

@CDB - and why can't it be used as water? Chemically and hence biologically it's one and the same thing. The extra neutron goes unnoticed. In fact, D is naturally occurring in (tap) water afaik.

Yeah. Tritium is the only relatively stable hydrogen isotope(half life of 12 years) that would be noticed when it changes from T2O to He2O or from THO to HeHO. This would give us helium dioxide and helium hydroxide both of which are unstable.

@Christiaan - Not quite. Since deuterium is among the heaviest of stable hydrogen isotopes, its bond to oxygen is much stronger. In small amounts, this is fine, but if you replace 50% or more of a higher organism's water with deuterium oxide, it results in cell lysis and ultimately the death of the organism because it cannot perform its regular biochemical reactions with such powerful hydrogen-oxygen bonds in place.

@CDB I don't think anyone has ever tried drinking 100% ethanol, glycerol or heavy water. I have heard (but not seen) that traditional wrestlers from Indian subcontinent drink a substantial amount clarified butter (ghee) which is 100% fat. Normal people can consume a few teaspoons without much problem.

Is there anything a human can drink that does not contain water?

Yes, there are a lot of liquids that do not contain water, but mostly they are not safe for human consumption.
Mercury is a liquid at room temperature. Can a person swallow it? Most assuredly. Motor oil has no water in it. It's not a satisfying beverage. Canola oil, olive oil, and many other food derived oils can be imbibed in even reasonably large amounts, but it won't do your digestive tract a big favor.
I've treated goats with propylene glycol (a liquid), parents treat their kids with mineral oil for constipation, etc. etc.
It depends on what you mean by "drink".

The previous poster is close to true but olive oil, canola oil, and any vegetable oil does indeed have water in it. It's small traces but the vegetables themselves feed off water and makes it way into the oil. https://www.oliveoilsource.com/page/what-olive-oil Motor oil indeed has no water. Mercury as well has no water.

@Sean, you could heat up some edible oil to remove water traces, and it would still be edible.

Add in 100% pure Ethanol, it will hurt like hell, is really hard to obtain but yeah. you can drink it allright.

Also add pure acetone. There have been cases where humans ingested significant volumes of it and lived.

I actually like this question.


text:
How does the glycocalyx of cells attach together if they are negatively charged?
Context

Thus, the entire outside surface of the cell has a loose carbohydrate coat called the glycocalyx.
The carbohydrate moieties attached to the outer surface of the cell has several important functions:

Many of them have a negative electrical charge, which gives most cells an overall negative surface charge that repels other negatively charged objects.

The glycocalyx of some cells attaches to the glycocalyx of other cells, thus attaching cells to one another.

[Guyton and Hall, Textbook of Medical Physiology, 2nd South Asia Edition ( w.r.t 13e)]
Here, two contrasting statements are written. They seem to differ in the context. Actually, I tried searching for more about glycocalyx and saw the same written in many places without explanation. I cannot understand that how the cells can be attached, if both of them are negatively charged.

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


text:
Why are we able to differentiate between colored objects without the presence of light?
Rods help us to see during the dark.
We can see colour of the object when it reflects light.
But in a dark room(room of any color but the light is switched off and it is night),we still can differentiate between colored objects if we open our eyes for sometime.(although not very much clearly)
How the colors are seen when there is no light?
Do we see as the brain remembers their colour?

Any room that is not pitch black still has light in it, what exactly is your definition of a dark room?

@Mesentery if you can see anything at all, then there must be some light.

The premise of your question is wrong. The colors aren't seen when there is no light. In a dark room where you can see things there is light, that's why you can see things in the first place. We don't just need light to see color, we need light to see in the first place ! I'll answer your question though since you seem sincerely confused.

Yes, because there is still light. Coming from the window, any lit electronics, seeping between the door frames, what have you. If you can see, there is light. (the brain can confabulate stuff when it has nothing to work with but unless you're in true mental distress you can usually tell that apart from actually seeing things (usually; it IS easier to mistakenly identify things in the dark)).

@mesentery writing @ the close voter will not work here ;)

To everyone voting to close: http://meta.biology.stackexchange.com/questions/2961/voting-to-close-a-question-as-off-topic-because-it-is-based-on-a-faulty-presuppo

You seem to have many misconceptions about how we see and how that relates to light. I'll address them one sentence at a time:

Why are we able to differentiate between colored objects without the presence of light?

Answer: the premise of the question is wrong: we aren't able to differentiate between colors without the presence of light, because we aren't able to see without the presence of light. Light is what allows us to see. "Seeing" is the act of detecting the light coming from the environment and using it to derive what the environment is like.

Rods help us to see during the dark.

It sounds a bit like you think rods help us to see during the dark... without light ? This is not the case: BOTH rods and cones absorb light and thus allow us to see. Rods help us see in low light because they are more sensitive (to light !) than cones. Nothing can help us see with no light.

We can see colour of the object when it reflects light.

It depends on how much light it reflects ! The correct form of that sentence is "We can see the object when it reflects light". (even more correct would be "when it reflects enough light to trigger the light receptors in our eyes, i.e. rods and cones). Whether we can see its colour depends on whether it reflects enough light to trigger the cones specifically.

But in a dark room(room of any color but the light is switched off and it is night),we still can differentiate between colored objects if we open our eyes for sometime.(although not very much clearly)

Indeed; this is because no room is completely dark. Even more so in our artificially lit world, but even in a moonless cloudy night you may have a few errant photons coming from the stars and Sun (via diffusion in the atmosphere), fireflies, what have you; to be fair in our artificially lit world I haven't experienced it. As far as I know you can get true pitch darkness in things like underground caves (once you're far enough from an exit of course).
Basically, if you can see anything then there is some light. (well, short of your optical cortex confabulating stuff, which in fairness it will do).

How the colors are seen when there is no light?

As I hope you understand now, they aren't.

Do we see as the brain remembers their colour?

I think that may actually be one reason we perceive colour in low-light environments. I'm sure some of it is that there's enough light to trigger the cones a little bit, but I wouldn't underestimate our brain's ability to show us the world as it knows it is as opposed to as whatever information it's receiving right this second says it looks like.
EDIT
Some references :
The state of seeing things in such low light that we only use the rods is called "scotopic vision" :
https://en.wikipedia.org/wiki/Scotopic_vision
Some sources for how "dark" environments still contain low amounts of light (one word for "amount of light" being "illuminance", measured in Lux) :
http://www.engineeringtoolbox.com/light-level-rooms-d_708.html
https://en.wikipedia.org/wiki/Aphotic_zone (thank you to @Johnny for that one)
HOPEFULLY LAST EDIT
On reflection I thought I'd say some more about scotopic vision since it's very relevant to the question. It turns out "scotopic" vision is opposed to "photopic" vision (the vision we have in full lighting, where the cones do the work because the rods are saturated), and in between there is an intermediate range called "mesopic" vision, which is likely the kind of vision we experience when it's dark but we still see color (this is ignoring our brain filling in colors, which could also be a factor and in that case could also happen with scotopic vision - but I didn't find any sources on that).
Mesopic vision is used under lighting conditions that seem to range from low indoor lighting or streetlights to starlight; scotopic vision is used with luminances darker than that. This page is all about it and includes a very nice drawing, sadly it's a pdf so I can't show it in the answer:
http://www.visual-3d.com/Education/LightingLessons/Documents/PhotopicScotopiclumens_4%20_2_.pdf

@Mesentery : that was harder to look up than I expected, but this looks good: http://www.engineeringtoolbox.com/light-level-rooms-d_708.html  it shows a table with the illumination in different environments. As you can see the lowest number it shows, for an overcast night, is not zero. It doesn't give numbers for a dark room though. Another reference I found to the concept: https://en.wikipedia.org/wiki/Scotopic_vision (turns out "seeing under low light" is called "scotopic vision", this gives specific illuminances as well).

@Mesentery I support Rozenn Keribin's answer that it is next to impossible to find a room that is aphotic (free of light) on the surface of the earth. Perhaps, the way we define the aphotic zone in Oceans (less than 1% of light) suffices as a reference? See article: https://en.wikipedia.org/wiki/Aphotic_zone

@Mesentery Done, and you're welcome !


text:
What happens to tube nucleus of the pollen tube after fertilisation?
Background:
Pollen tube contains a vegetative cell and a generative cell. The vegetative cell contains the tube nucleus, and the generative cell contains two male gametes. The two male gametes fuse with the egg to form the embryo and with the polar nuclei to form the triploid endosperm in angiosperms.
Question:
What happens to the tube nucleus of the pollen tube after/during fertilization?
Research:

This site says that the tube nucleus disintegrates.
This article does not mention about disintegrating nor discuss anything about the fate of tube nucleus.

Short Answer: It disintegrates.
Background: Although I was unable to find any primary reference, there were many secondary references stating that the pollen tube does disintegrate. In very short, after the pollen tube reaches the female gametophyte, the pollen tube nucleus disintegrates. For the 'why', it disintegrates to let the two sperm cells pass through, and also since its function of controlling the growth of pollen tube has finished.

For citation, you can have a look at:

Fertilization - Wikipedia
Advanced Biology -
A new mainstream text for the new specifications
Advanced Science; Michael Kent, 2000
Sexual Reproduction in Angiosperms; Kimball's Biology Pages
BIOPL 2410 Introductory Botany; KNiklas, TSilva; Cornell University
The Structure and Functions of Flowers - LeavingBio.net (image source)


text:
Can someone identify this plant
Growing in a garden in the philippines
Photo from above notice the unusual leaves

Photo showing bloom... In peak bloom...

Photo showing pod that plant produced at the same time blooms appeared

What is the word for the leaf structure - meaning secondary terminal leaf at the end of a "tendril"? The plant form somehow reminds me of a Nepenthes, but the terminal growth is a leaf not a pitcher.

@user22542 I thought this could be called "mucron" in French, but I don't know in English (from what I've found, "mucron" exists in English but has a different meaning).


text:
How can I differentiate between polysaccharide bands and protein bands on SDS-PAGE?
I tried to extract bacterial polysaccharide but after running a SDS-PAGE I couldn't differentiate between the polysaccharide band and protein ones. I face a problem of moving up of the samples from the will and no clear bands. Any suggestions?


text:
Are mutations accumulating far faster than selected out?
I just want to see the mutation accumulation rate in human populations. Versus the rate at which mutations are selected out. Just wanted to check if the genome is deteriorating

Welcome to Biology.SE
Is the rate at which new mutations occurring higher than the rate at which alleles fix today in humans?
Human populations are exploding! Genetic diversity within a population is a function of the effective size of its population. As the population expansion in human is extremely recent, we ought to expect that our genetic diversity is much lower than what would be expected from our population size and structure. Therefore, yes, genetic diversity is currently increasing, or in other words, more mutations appear than there are alleles that fixed.
Is the genome deteriorating?
I am not sure what you mean by "the genome is deteriorating" but the answer to "Is the genome deteriorating?" is likely no!
Actually, larger populations tend to suffer from less drift load and as such our mean fitness would rather be increasing. However, given the population size, I doubt that would make such an important difference.
On the other hand, medicine is greatly affecting our environment and is reducing the strength of purifying selection. As a consequence, modern populations would eventually be less fit than our ancestors if placed in the environment experienced by our ancestor (that is an environment with little to no medicine). But this will not be true in our current environment.
Prerequisite to understand the answer
This answer felt quite introductory but it actually contains all the following concepts:

Allele
Allele fixation
Genetic drift
Effective population size
Population structure
Drift load
Purifying selection
Genetic diversity (typically defined as the expected heterozygosity)
Effective population size
Environment (and even niche construction)

If any of the above concept is unclear to you (and I very much suspect that at least the term "drift load" will be new to you), then you might want to start with an intro course to evolutionary biology and population genetics.

Yes it is of course deteriorating, as can be proven with simple math, see for example Lynch (2009) or this later paper by Lynch (2016).
Thus, although there is considerable uncertainty in the preceding numbers, it is difficult to escape the conclusion that the per-generation reduction in fitness due to recurrent mutation is at least 1% in humans and quite possibly as high as 5%. Although such a mutational buildup would be unnoticeable on a generation timescale, over the course of a couple of centuries (approximately six generations), the consequences are likely to become serious, particularly if human activities cause an increase in the mutation rate itself (by increasing levels of environmental mutagens). A doubling in the mutation rate would imply a 2% to 10% decline in fitness per generation, and by extension, a 12% to 60% decline in 200 years.

So, this means about 6000 years after the world was created we'll be unfit to do anything? ;)

@JollyJoker I am not sure what you are referring to when you talk about the creation of the world but if you refer to either the big bang or the agglomeration of matter that ended making earth what it is, then there was no life 6000 yet years after that event. There was therefore no "we" whatever "we" may refer to in your comment.

@Remi.b Just jokingly referring to young Earth creationism

@JollyJoker Fair enough. I should have known given your user name!


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Are these images of carpenter ants?

When I searched carpenter ant in Google, this looks kind of like some of the images. Some other images show reddish or winged ants and I have not seen any of those.
I've seen 3 or 4 of these big black ants in the last month we've been in our new house, wondering if I should be concerned.

Which country is this one from?

@Nakx - this is in the United States, Minnesota.

There are probably a few similar species that are hard to distinguish, but Camponotus pennsylvanicus is a common black Camponotus in the USA.

Hmm, the picture that you shared has ants with a striped abdomen, a characteristic feature of Carpenter ants.

(source: doyourownpestcontrol.com)
Wikipedia seems to confirm the same thing.
Carpenter ant
So I would say yes, this is a carpenter ant.

It is a Camponotus, but other genus also have striped abdomen (Formica for example).


text:
What is this flying animal that hovers like a hummingbird?
What is this animal?

Characteristics:

Has a long curved bill.
Has green upper body and a dark black lower body.
Likes petunias.
Hovers like a hummingbird but is a bit smaller.
Has small rear feather-like tufts and is very odd shaped.
Moved quickly from flower to flower.


text:
What is this worm or larva I found in my walls
We were recently doing some major remodeling in our 1920s era home and found what looks like a nest of small meal worms. I am wondering if anybody can identify them! Here are some photos:

Our home is in Denver CO. I didn't see any living examples so it is possible they have been there for nearly 100 years.


text:
Help! What kind of spider is this?

Can anyone tell me what kind of spider this is and if it might be poisonous?

Welcome to Biology.SE! Please provide the location and an approximte size of the species. A close-up photo would be much better.

looks like it was a broad-faced sac spider, or something related


text:
Does the cactus wren use a call to elicit insect prey movement and detection?
I will be referring primarily to a 2013 paper, If a bird flies in the forest, does an insect hear it?, and my own investigation. Bird flight sound frequencies overlap with the hearing range of most tympanate insects. There are several insects that possess hearing for which the function is not known and it is hypothesized that this capacity is used to avoid predation. For example, silent butterflies and grasshoppers have broadband audio sensitivity and some calling insects appear to have hearing tuned outside of the call frequency.
I have observed cactus wrens (Campylorhynchus brunneicapillus) foraging for insects on the ground outside my window (southwest desert, USA) and have noted that they invariably emit a characteristic odd periodic call while they are so engaged. You can hear my recording of one such hunting wren made April 18, 2017 here. Cactus wren foraging call
I used the open source audio processing application, Audacity, to analyze the wren call I recorded. Here is a spectrogram of the call:
.
You will note that the call is periodic at about 7 Hz. For comparison, typical pulsed bird wing sounds (the sound of bird wings as they are hovering or approaching prey) are around 18 Hz frequency. Those wing sounds are broadband bursts though, approximately 49 kHz +/- 18 kHz. I mention this because the cited paper and many others looking at bird sounds and insect hearing have explored primarily the hypothesis that it is the flight sound the insects are detecting. My own idea is that some bird species actually generate sounds within such a range in order to provoke prey insects into fleeing from hiding or a stationary position.
Typical moth and butterfly audio frequency response is given here:

(reproduced from the work cited earlier).
The cactus wren call may be seen to exhibit energy in the 1.6kHz - 2.20kHz range primarily, peaking at 1954 Hz (spectrographic analysis of exactly that portion not shown). This seems interesting given that Cyphoderris crickets call at 12 kHz, but their ears are most sensitive to 2 kHz (almost exactly the wren burst frequency peak).
I could not find research examining my hypothesis and thought I would ask the question here, i.e., is there research examining the possibility that certain bird species use calls to enhance detection of prey insects (and the related question, does this seem likely given what others may know about the subject of insect hearing, its range and uses, bird predation behavior, etc.)?


text:
How can I perform a 1:1 sequence-structure alignment for a pdb template dimer and homologous dimer sequence?
I have:
1. A PDB dimer protein structure template of a real solved protein.
2. An unsolved, but highly homologous dimer protein (>90% sequence identity.)
How can I use MODELLER to make a theoretical model of my dimer of unknown structure, using the homologous dimer template?
I know I need a PIR alignment file, probably with a 1:1 sequence-structure alignment.  However, I do not know how to make this file.
Please advise?


text:
Why are VAL, MET and ALA substitutions commonly used for protein behaviour and function studies?
I have seen that amino acids are commonly replaced with VAL, MET or ALA to study the effects of these specific substitutions.  Why are these specific amino acids used in particular, what are the results of these substitutions expected to show, could substitutions of other amino acids achieve the same results, and what is the source of this technique?

It highly depends on what you're trying to look for with your mutation as to which substitute you use.

Substituting a single amino acid and checking the effect this has on a protein is a method to determine what this specific amino acid does in the protein. For example, substituting an amino acid that is part of the catalytic core would almost always make the protein non-functional.
Alanine scanning is a technique that methodically replaces amino acids in a protein with alanine. Alanine is probably the most neutral substitution, you essentially remove the amino acid sidechain. Glycine for example would be problematic because it is more flexible and can adopt secondary structurs other amino acids can't.
If you want to find out what a specific amino acid does, you don't want to introduce any other new effects when mutating it. Depending on what exactly you're looking at, substituting other amino acids is certainly possible. Some changes to alanine might be too drastic and you might want to substitute an amino acid that is more similar to the original one. This all depends on what exactly you are looking at.


text:
What is the significance in an alpha-helix being right-handed or left-handed?
Why is that often when alpha-helices are discussed, it is also mentioned their direction - right-handed (clockwise) or left-handed (anti-clockwise)?
I have heard that left-handed alpha-helices are usually less stable, but I'm sure there is more to it than that?

A quick search sent me here: https://www.quora.com/Why-are-most-alpha-helices-in-proteins-right-handed .

Some experimental and modelling observations suggests, folding energy for right handed in more favorable. You can find more detailed answer to this question here.


text:
Are multi-chain proteins synthesized as one biological unit?
Are multi-chain proteins (especially homo/hetero-dimers) synthesized together as one overall unit or are they separate monomers which bind together at some point after synthesis, and are there any relevant factors to know about this process?

Big broad question. Each protein is slightly to greatly different. Generally they are individually folded and brought together by chaperones or proximity.

The question is fine in my opinion.

Are multi-chain proteins synthesized as one biological unit?

Sometimes yes but mostly not.

Some proteins are synthesized as one long polypeptide pre-protein which is cleaved by some proteases to yield multiple chains. After cleavage the intramolecular interactions become inter-molecular or inter-chain interactions. Insulin is a good example of this (See the figure below).

In other cases the chains are synthesized as different polypeptides which (with or without processing) subsequently associate with each other. In case of homo-multimeric proteins, the polypeptides are made by the same mRNA.

Nice answer from WYS. I would have been inclined to say that the ribosome translates one polypeptide and any associations happen post translation. Insulin is interesting in that one polypeptide is produced and then cleaved to form components of the protein so that one could say multiple parts are made at the same time if I understand this correctly. Generally the complexities of a protein are introduced after the ribosome has done its job of translation to form one string of amino acids. Protein interactions are a matter of great interest now. I'm not sure one can say any protein is formed independently but is more part of a large ochestra.


text:
How is Glycophorin A and straphylococcal related to Escherichia coli and what does readily purified mean in this context?
I am reviewing the paper "Glycophorin A Dimerization Is Driven by Specific Interactions between Transmembrane Alpha-Helices."  There is a statement in the abstract which I don't understand:
"The transmembrane alpha-helical domain of interest is fused to the C-terminus of staphylococcal nuclease.  The resulting chimera can be expressed at high levels in Escherichia coli and is readily purified."
As I understand it, this describes that an alpha-helix within Glycophorin A is fused to straphylococcal nuclease?  Then, how does Escherichia coli come into the discussion and what is meant by being readily purified?

Basically, they engineered a vector which, when transfected to E. coli, produces transcripts of -and thus proteins to- a fusion gene which produces these transmembrane α helices conjugated to the staphylococcal nuclease. In other words, the E. coli are just factories for producing proteins:

Expression, Extraction, and Purification of SN/GpA - For high
  levels of SN/GpA production, pT7SN/GpA was transformed into E.
  coli MGT7 (kindly provided by D. LeMaster), containing the plasmid
  pLYS-S.

And the reasoning therein was proposed in the discussion,

We report here the use of a chimeric protein to show that
  the presence of just the transmembrane domain of GpA, fused
  to a normally monomeric soluble protein, is sufficient to
  mediate the dimerization of this artificial membrane protein
  -in SDS

What they mean by readily purified is that the protein can be extracted relatively easily, and in the experimental method they explain some commonplace methods of purification:

One-step purification of milligram quantities of SN/GpA from the
  extract could be achieved by reversed-phase HPLC utilizing an acetonitrile/isopropyl
  alcohol/water gradient on a semipreparative Vydac
  C4 column. Alternatively, purification of larger quantities was
  achieved using two rounds of cation-exchange chromatography...
...The chimera SN/GpA131, but not truncated forms, could alterNaCl,
  50 mM Tris-HC1, 5 mM EDTA, 1 mM PMSF, 0.025% NaNa,
  natively be extracted by sonication of the pellet after cell lysis in 1 M
  pH 7.9, containing no detergent. This extraction was of similar
  efficiency to that with Lubrol, and was utilized in the preparation of
  material for generation of transmembrane peptide by trypsin treatment.


text:
Core architecture of the body encoding
First of all, I am not a biology guy; I am in Computer Science. But, I have a strong interest in all the mysteries of nature, from universe to human body. So, I want to ask a question related to genetics.
As I have read that all(both male's and female's) the biological traits of a person are passed genetically to the offspring(of course assuming the crossing). So if my mom's eye color is blue and my dad's eye color is also blue, I will get blue color too, but what about the core architecture of the body? I mean I have 2 legs at a certain location from my body(my waist but, not from my head!) and similarly other orientations. Why they are that certain way? If they somehow got changed, would the resultant body be stable?Is the answer different in case change is artificially engineered or natural?
Where is this core architectural information exactly stored(If the answer is DNA then how?) and in what form is it stored?How come that information is not changed in thousands of years or even millions of years? And is that information of such nature that it contains "exact" steps to develop a healthy say, brain structure(which is a really complex)?
My another question is: If there is a community of mutated people, will their offsprings be mutated always with 100% certainty?
I know these are a lot of questions but you can see that, they basically revolve around the information that I am curious about. Can someone address my curiosity?

Welcome to Biology.SE! And thanks for sharing your question. I think it may hold potential, but it needs some work I think. Most importantly it is a stack of broad questions. Some research from your own may help to pin down a good question.

@ChrisStronks: Yeah, sure then you may give me some pointers

It's your question, your call. Just trying to help.

Btw, the Biology community here is so small compared to Computer Science community!

Perhaps you'd like to read a popular science book about genetics and development, as it is really the intersection of these two fields ('developmental genetics') that is concerned with how an ordered body arises from a fertilised egg and its genetic information.
It's a fascinating question, I feel it might be too challenging to cover properly on this website.
Try "Endless Forms Most Beautiful" by Sean B Carroll, to learn a little about embryo patterning and homeobox genes. Historically scientists studied frankenstein-ish developmental mutants with disordered body plans. It's a complex system

For my two cents', as regards body structure development specifically, genes don't code for final shape but for the developmental process; in some ways, it's abstractly similar to the development of a fractal. The sheer number of genes which can come together to create a single particular result further complicates things.

Welcome to Biology.SE!
Your question is very broad. Also, your post has the default of containing severals questions in it. Make sure in the future to restrict your post to only question, it will be much more likely that you receive a good answer then. I hope that I can give some indications about how to get some more knowledge in this answer. In this answer, I do not consider all your questions one by one to answer them (or guide you to the answer) but I think that all your questions will get an answer as you learn more about the subjects I cite. Hope that answer will help you.
Very basics of molecular genetics
You should start to have a few ideas about genetics. Make sure you know what is a chromosome, a gene, an allele, a protein and a phenotype. Wikipedia will help you with that. Come back on Biology.SE if something seems unclear to you.
Basics of genetics and evolution
You are definitely interested in concept of segregation. This is a very fundamental concept in genetics. The basis of the laws governing segregation has been first discovered by Gregor Mendel and we still name these basics laws after Mendel. We talk about Mendelian segregation. You may want to google that.
Then you are interested in the concept of heritability. I have been talking about heritability in different posts. In the third sentence of my answer here, there is a short list of posts that define the concept of heritability.
Eye color you said?
You talked about the genetics of eye color inheritance. Here is a post that will interest you then.
The Genetics of Development
Your question is not only about genetics but is about the genetic of development. You may want to have a look to the basics of developmental biology. The most famous DNA sequence  involved in determining the body plan of many different living things are the so-called homeobox. There is plenty of interested things about this homeobox. This post may interest you btw.
Rough details about the evolution of development along the tree of life

How come that information [architectural information] is not changed in thousands of years or even millions of years?

It really depends on what you call architectural information. But in any case it does evolve. If you think of things such as like size of an animal. Then it may evolve fairly quickly. You may thing of more important change, such as evolving a new pair of legs or evolving wings or a head, then it tends to take more time. Below are just a bunch of examples of how animals differ in terms of body plan along the tree of life.
You might be interested to study a bit the development or early animals. Some have a radial symmetry while other (like us) have bilateral symmetry (see wiki). Some animals have a head, some don't. Some animals have two dermes while others have three dermes. The Deuterostomata (vertebrates, tunicates, echinodermes, ...) have a development where the blastopore of the gastrula becomes the anus while in the protestomata (now thought to not be monophyletic and divided into ecdysozoa and lophotrocozoa (see here)) the blastopore becomes the mouth. Among the arthropoda (insects, spiders, millipedes, ...) the story is very interesting as well. Some have a highly segmented body with a pair of legs at each segment (millipedes) while other groups have fused those segments. Spiders have only two big body parts, while insects have three big body parts. In insects, the thorax (one of the 3 body parts with the head and the abdomen) contain three segments and each segment hold a pair of legs. The first flying insects also had three pairs of wings, now degenerated into two and even into one in Diptera.

Hox genes are found on chromosomes 2, 7, 12 and 17. They are also not the only genes to contain a homeobox.

Oops. That's not what I had in mind but I know little about the subject. I corrected it my answer. Please let me know if my answer there contain mistakes!


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To what extent are microtubule-filaments present in astrocyte leaflets?
I have been trying to find information about whether microtubule filaments are present in the leaflets of astrocytes. A astrocyte can have quite varied morphology but many at least, have a star-like shape, with multiple branches, that become progressively branched into thinner processes. I found a suggested terminology for the progressively thinner branches here: Diversity of astrocyte functions and phenotypes in neural circuits
Soma --> Branches --> Branchlets --> Leaflets
The leaflets are really thin, maybe around 200 nm in width, and contact synapses at the "tripartite synapse".
What I'm curious about is whether there are microtubule filaments extended into these thinner leaflets. I know they are present in the branches and branchlets. But since MT filaments are around 25 nm in width I was thinking they were maybe too thin. I also read in a A closer look at astrocyte morphology: Development, heterogeneity, and plasticity at astrocyte leaflets saying that "The peripheral, leaflet-like processes which comprise much of the astrocyte volume exclude these large filaments and instead rely on actin dynamics for their structure, much like neuronal spines" But when I read the referenced article I couldn't find the authors making any similar conclusion...so I don't know, I'm really curious about this, if anyone has any idea, intuition, or facts (though I'll welcome any hunch) that would be greatly appreciated!


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Do Tardigrades have an innate immune system, or any type of immune protection?
Do Tardigrades have any immune protection against bacteria and viruses?

Welcome to SE Biology. Please read the Help on Asking Good Questions. A one-liner starting with an obvious typo (repeated in the title) hardly corresponds to providing context and demonstrating an attempt to answer the question yourself.

I could not find any data on their surival following an infection compared to uninfected individuals. I could not find a proper description of their immune effectors either. However, I would be very surprised if Tardigrades did not exhibit immune reactions in the case of a sceptic wound.
They are exposed to many different bacteria in their environment, which affects their own microbial communities, and even seem to have endosymbionts:
https://par.nsf.gov/servlets/purl/10217788
Endosymbionts are usually kept under control by the immune system in insects. I expect it to be the case in tardigrades.
They do not seem to possess the classic pathways leading to antimicrobial peptides production in other ecdysozoa, although in their genomes you can find other NF-κB distantly related NFAT homologs:
https://academic.oup.com/g3journal/article/10/3/1137/6026230?login=false
In this paper : https://www.biologie.hhu.de/fileadmin/redaktion/Fakultaeten/Mathematisch-Naturwissenschaftliche_Fakultaet/Biologie/Institute/weitere_und_ehemalige_Dozenten/weitere_Dozenten/Prof._Dr._Hartmut_Greven_i._R/2005_04_2005-Greven-Dastych---Kraus-integument.pdf
there is a picture of their hemocytes, which in insects have an immune function.
I could find mention in several papers of a pigment resembling melanin, which in insects (as well as a lot of other clades) has an immune function.
More evidence might come, although I would assume their size to make experimental infections and RNA extraction  (in order to detect upregulated genes) very complicated.

Does this actually answer the question? I'm asking because I could not find any papers that actually concluded that they do have any immunological capabilities, and that the genes comparable to those of other organisms' immune systems might have been conserved for other reasons. Thanks. (My takeaway was, "They might, but we don't know yet." However, I have only the most basic understanding of immunology.)

You are right, this is more my opinion based on the information I could find. I rephrased my answer.


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Sense of rotation of DNA motors
DNA motor will rotate during transcription instead of reciprocal.

What others will rotate?
Does it rotate in a fixed sense?
Why do they rotate?


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Which organism built this 2 cm long sandy tube?
I found this tube and wondered which animal built it.
It is 2 cm long and has an entrance/exit hole on one side. The material seems to be sandy.
I assume it is for breeding purposes.
Before finding the tube, I saw an unfamiliar kind of wasp around (could also be a hornet), with very long black legs. However, I could not find a wasp or hornet that builds such tubes, so it could be unrelated.
Location is Germany.
My questions are: which organism built this structure and should I expect anything crawling out one day? Or is it unfinished, since the entrance isn't closed?

Just found this post, which seems to be related: https://biology.stackexchange.com/questions/49088/what-wasp-like-insect-breeds-in-clay-pots-with-dead-spiders

This is the nest of a Mud dauber, also known as Mud wasp. This was possibly made by a Black and Yellow Mud dauber based on the following information.

The nest of the black and yellow mud dauber is a simple, one-cell, urn-shaped nest. 1*

As for expecting something coming out of it? I doubt it, as the nests are sealed after depositing an egg.

After building a cell of the nest, the female wasp captures several spiders. The captured prey are stung and paralyzed before being placed in the nest (usually 6-15 per cell), and then a single egg is deposited on the prey within each cell. The wasp then seals the cell with a thick mud plug. 2*
Eventually, the hatching larva will eat the prey and emerge from the nest.

You are right. Just saw mommy coming back to continue her work :) Interestingly, they were introduced in Germany in the 70s/80s.

@another'Homosapien' Quoting sources [1][2]: "Not normally aggressive, but can become belligerent when threatened." & "Stings are rare due to their usually peaceful nature, however nests are aggressively defended."

This wasp is thought to be responsible for the deaths of over 180 people when an airliner crashed after the wasp built it's nest in a tube - https://en.wikipedia.org/wiki/Birgenair_Flight_301


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Chlamydomanas are present in Kingdom Protista or Plantae?
Chlamydomonas, Chlorella are present in Kingdom Protista as well as  Plantae under division algae.
In which kingdom they correctly belong to?

It is generally accepted now that Chlorophyta are Plantae (see here). They are more closely related to plants than any other group of organism. Protist is a kind of basket term for any eukaryotic unicellular organism that is not an animal, fungi or a plant which is a rather exclusionary definition.
Personally, I think the kingdoms are pretty 'macro' oriented and do not really capture the diversity well of unicellular organisms. If you want to see a bunch of elderly scientist shout at each other over what appear to be arbitrary distinctions, I highly recommend attending the taxonomy session of any unicellular conference

What about Rhodophyta and Phaeophyta?? BTW Thnx;)

The rhodophyta might be monophyletic with the green lineage (have a common ancestor) but the Phaeophyta are definitely distinct and they likely arose during a seperate endosymbiosis event. They just do not fit in the five kingdoms. http://www.algaebase.org/ is quite respected for questions of algae taxonomy


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Longest transcripts without isoforms
Does anyone know what genes produce the longest mRNAs? I am planning a project on synthetic introns and want to use stuffer fragments to vary intron size. Obviously they must not contain any splicing sites, hence I plan on buying cDNA clones.
It would be incredibly appreciated if someone could point fingers at transcripts that are 12...20 kbp long (and ideally have no other known isoforms or cryptic splicing sites).
Thank you!

In which organism? BTW, since you're ordering cDNA anyway, I imagine most of the non-cryptic splice sizes will be gone anyway.

mammalian, prefferably mouse

Do you mean "longest transcript without introns"?  if you want a gene with only a single isoform, I'd parse the latest mouse gtf, and look for genes with only a single transcript line.  You can get the gene length (though oddly enough, not the transcript length) in there too.

These question here is refering to the longest cDNAs. No matter if they contained introns before. The final product mustr not contain any splicing sites

To R!

Download the most comprehensive GTF file from Gencode for mouse.
Do the following in R (I'll put comments in the code so you can hopefully follow along):

library(GenomicFeatures)

#Load the GTF file and make a TxDb object
txdb = makeTxDbFromGFF("gencode.vM13.annotation.gtf", format="gtf")

#Make a GRangesList, with transcripts split per gene
grl = transcriptsBy(txdb, by="gene")

# Filter the GRangesList for genes with one annotated isoform
grl2 = grl[which(elementNROWS(grl) == 1)]

# Make a new GRangesList of the exons per gene from above
grl = exonsBy(txdb, by="gene")
grl = grl[which(names(grl) %in% singleIsoformGenes)]

# Get the length of each single-isoform gene
lens = sum(width(grl))

# Get the top 10 single isoform genes by length
head(lens[order(lens, decreasing=T)], n=10)

You then get the following output, with gene IDs on top and lengths below that:
ENSMUSG00000020255.8 ENSMUSG00000101609.1 ENSMUSG00000104211.1
              123179                84395                74456
ENSMUSG00000109536.1 ENSMUSG00000109125.1 ENSMUSG00000047888.9
               30942                25241                17327
ENSMUSG00000022262.7 ENSMUSG00000066108.7 ENSMUSG00000033826.9
               15630                14964                14583
ENSMUSG00000032855.5
               14170


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Why do people with type O blood have anti-A and anti-B antibodies?
People with type O blood have anti-A and anti-B antibodies, even without receiving a transfusion. Why?

@GerardoFurtado — Take the bull by the horns and rewrite the question to fit your answer, otherwise the whole thing is meaningless and is likely to be shot down as such. Are you sure the question has not already been asked?

Similar to https://biology.stackexchange.com/a/5724/1320

even though @GerardoFurtado 's answer is very interesting, i think it fails to explain why there are the antibodies there in the first place. so if that was your question, i posted my answer to it!

Antibody-producing cells (B lymphocytes) generate antibodies through a gene recombination process, that allows a virtually infinite number of antibodies to different antigens to be created, including against self-antigens (https://en.wikipedia.org/wiki/V(D)J_recombination).
A process of maturation, if working correctly, allows for those cells producing antibodies that strongly bind to self-antigens to be suppressed or eliminated, preventing autoimmune attacks (https://en.wikipedia.org/wiki/Immune_tolerance). In this process, specialized cells present a myriad of self-antigens to the maturing lymphocytes, signalizing them to undergo apoptosis or become regulatory cells if they bind to them. Organisms with the A antigen will present it to maturing lymphocytes and thus create tolerance to it, not having cells producing A-antigen binding antibodies; but they don't have the B antigen, so their lymphocytes won't be selected over it, and they will have cells producing B-antigen binding antibodies, which, if such antigen is introduced into the body, will mount an immune response against it.
Likewise, someone with an O type blood won't have both the A and B antigens, and so cells producing antibodies that bind to them will be allowed to mature, and they will have anti-A and anti-B antibodies circulating in the blood.
In conclusion, we can and do have antibodies for more antigens than we will ever encounter, and we have then before ever encountering them. If we do encounter them, then the cells that produce those antibodies will multiply and the number of those antibodies will greatly grow. Typically, we only don't have antibodies for self-antigens.


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Can bacteria be considered carnivores?
Ok carnivores are "animals that eat other animals," so what are bacteria that eat animals? Or are they just not important

I think it's more that bacteria are a special case. As they don't directly consume anything, taking the so-called "flesh eating bacteria that cause necrotizing faciitis as a good example: they simple release compounds or toxins that break down the surrounding matrix or tissues and absorb the products. In that sense you could call them saprophytes, saprovores or saprophages: organisms that consume decaying organic matter.

Welcome to Biology.SE! "carnivores are animals that eat other animals" well, its a bit different. A carnivore is an organism that derives its energy and nutrient requirements from a diet consisting mainly or exclusively of animal tissue, whether through predation or scavenging. Bacteria ain't that choosy, are they?

I'm voting to close this question as off-topic because it is not about biology. It is an attempt to provoke a pointless discussion of semantics.

@David I disagree; understanding how technical words are defined in a scientific field and why those definitions were chosen is about as pointful as semantic discussions can get. It looks to me like there's the potential for good and informative answers there is what i'm saying. Unless "attempt to provoke a pointless discussion" is an informed statement about the OP's intentions (i.e. they're an outright troll) of course.

@RozennKeribin — I call them as I see them. You are entitled to your opinion, but I do recommend that you reread the tour to this site and especially https://biology.stackexchange.com/help/dont-ask, and then consider whether questions are or are not in the spirit of and useful to this site.


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How does tetracycline transactivator localize to the nucleus? Where is the nuclear localization signal?
Proteins typically use a nuclear localization signal (NLS) to localize to the nucleus. Tetracycline transactivator (TTA) needs to work in the nucleus, but I did not find an NLS in the structure.
Tetracycline transactivator is a fusion of tetracycline repressor of E. coli (P04483) and  VP16 of HSV (although by blast I only found P04483).

The Tet-Off system makes use of the tetracycline transactivator (tTA) protein, which is created by fusing one protein, TetR (tetracycline repressor), found in Escherichia coli bacteria, with the activation domain of another protein, VP16, found in the herpes simplex virus.2. Source

There can be multiple NLS's, but the ones I checked I did not find here.
Elements

TetR is a protein from  E. coli, which has no nucleus, and the above sequence is a perfect match to P04483, so NLS is not expected here.
VP16 is from HSV, and it is reported to use HCF-1 to locate to the nucleus.

VP16 itself does not possess a nuclear localization signal; it is transported to the nucleus by HCF-1 and then binds to Oct-1, which can also recognize the same target sequence.
- Since only a domain of VP16 is (f)used in TTA, I am not sure if this is present.

Vaysse 2013 explicitly added an SV40 NLS to TetR, although for a completely different reason (translocate the plasmid DNA in to the nucleus during transfection).

Sequence of Tetracycline transactivator (advanced)
tccagactggacaagagcaaagtcatcaactctgccttggagctcctgaatgaagttggcattgagggcttgaccaccaggaagctggcccagaagctgggtgtggagcagcctaccctgtactggcatgtgaagaacaagagggctctgcttgatgccctggccattgagatgttggacaggcaccacacccacttctgccctctggaaggggagtcctggcaggacttcctgaggaacaatgccaagagcttcagatgtgccttgctctcccaccgggatggtgccaaagttcacttgggcaccaggcctacagagaagcagtatgagaccctggagaaccagctggcattcctgtgccaacaaggcttctccctggaaaatgccttgtatgccctctctgctgtgggccacttcaccttgggctgtgtgctggaggaccaggagcaccaagttgccaaggaggagagggagacccccaccactgactccatgccaccactgctgcggcaagctattgagttgtttgaccaccaaggggctgagcctgcattcctttttggcctggaactgatcatctgtggcctggaaaagcagctgaaatgtgagtctggctctcacgtgcccaaaaagagaaagcacgtgcctgctgatgccttggatgattttgacctggacatgctgcctgctgatgccctggatgactttgatttggacatgctccctgctgatgcacttgatgattttgacctggatatgctg

I noticed after writing my original answer that your DNA sequence is not tTA (TetR-VP16). I've expanded my answer to account for this, but you might want to provide the source for your DNA sequence.

Hi! It is the Synthetic construct improved tetracycline-responsive activator mRNA, complete cds; GenBank: DQ414432.1

If you follow the authors' references you'll see that the sequence you provided is not tTA, but instead itTA (improved tTA). From PMID: 15548671:
The itTA sequence, generated by assembly PCR, encodes three F-domains (PADALDDFDLDML) in place of VP16

Proteins with a molecular weight less than ~30 kDa(*) can diffuse freely through the nuclear pore (see for example here (1) for a review on nuclear transport).
Assuming that the sequence you provide for tTA is correct (EDIT: it is not, see edit below), the protein would have a molecular weight of 28.64 kDa, i.e., below the size limit. In other words, it seems like an NLS is not essential for tTA entry into the nucleus, which is evident from this paper (2) where they use tetracycline to regulate expression from a tTA-dependent promoter in HeLa cells.
Having said that, in this paper (3) (unfortunately paywalled) they create a tTA-nls derivate of tTA by fusing an NLS (KRPRP) to its N-terminus. No data on nuclear localization is shown in the paper itself, but they refer to a thesis (4) where nuclear enrichment of tTA-nls has apparently been shown.
So, although tTA can enter the nucleus without an NLS, including one will cause it to actively localize into the nucleus, possibly improving its transcription factor activity.
(*) This is a number I've heard before, and apart from finding it in the review I haven't bothered looking up the original reference. There are more accurate ways (5) of defining the free diffusion barrier, but I'll stick to ~30 kDa for the purpose of this answer.
EDIT: I did a bit more research, and it looks like the DNA sequence you provide is incorrect. The first part does encode for TetR (2-207), but the second part is not something I could identify, but it is certainly not VP16 (see EDIT 2 below).
In the original paper (2), two versions of tTA are created. In both cases they use an N-terminal region of TetR (1-207):
>TetR (P04483) 1-207
MSRLDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEMLDRHHTHFCPLEGESWQDFLRNNAKSFRCALLSHRDGAKVHLGTRPTEKQYETLENQLAFLCQQGFSLENALYALSAVGHFTLGCVLEDQEHQVAKEERETPTTDSMPPLLRQAIELFDHQGAEPAFLFGLELIICGLEKQLKCESGS
They then use two different fragments of VP16 and fuse them C-terminally directly to the above TetR fragment:

Long VP16 fragment (363-490)
>VP16 (P06492) 363-490
AYSRARTKNNYGSTIEGLLDLPDDDAPEEAGLAAPRLSFLPAGHTRRLSTAPPTDVSLGDELHLDGEDVAMAHADALDDFDLDMLGDGDSPGPGFTPHDSAPYGALDMADFEFEQMFTDALGIDEYGG

Short VP16 fragment (406-490)
>VP16 (P06492) 406-490
HTRRLSTAPPTDVSLGDELHLDGEDVAMAHADALDDFDLDMLGDGDSPGPGFTPHDSAPYGALDMADFEFEQMFTDALGIDEYGGF
The trailing phenylalanine (F) in the second sequence is not part of the original VP16 sequence, but gets added as a result of their method of cloning.

As far as I can see, they only use the longer version of tTA in the paper, and show that it works in HeLa cells. This is despite the fact that this protein actually has a molecular weight of 36.92 kDa. This is above the ~30 kDa size limit I mentioned earlier, but since this limit is only approximate and tTA clearly works, I think it is still safe to say that tTA freely diffuses through the nuclear pore (albeit not as efficiently as a smaller protein might).
EDIT 2: after the Op provided the reference for the DNA sequence (GenBank: DQ414432.1), I was able to identify the ORF from this source paper (6) as  "improved tTA" (itTA), and the C-terminal fragment as three F-domains (PADALDDFDLDML).
References

Kim YH, Han M-E, and Oh S-O (2017) PMCID: PMC5509903.
Gossen M and Bujard H (1992) PMID: 1319065.
Gossen et al (1995) PMID: 7792603
Kistner A (1993) thesis, University of Heidelberg, Germany.
Matsuda A and Mofrad MRK (2021) PMID: 34339633.
Krestel HE et al (2004) PMID: 15548671.

Wonderful, thank you so much! It is a very clear and precise answer; much appreciated!


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What are the differences between a liposome and simple cell membrane
I'm learning about chemical evolution and the transition from RNA to protocells to cells.  I understand that the protocells have a phospholipid structure called a liposome.
I recently saw a video showing CG animations of the workings of a cell and it seemed that the cell wall was much more complex than what it seems a liposome is.
I'm looking for information about the differences between a liposome and a basic cell wall (not sure of the difference for different types of cells -
 but I guess for prokaryote since that would have been first.)

By looking on wikipedia I found:
About liposome

A liposome is a spherical vesicle having at least one lipid bilayer. The liposome can be used as a vehicle for administration of nutrients and pharmaceutical drugs. Liposomes can be prepared by disrupting biological membranes (such as by sonication).
Liposomes are most often composed of phospholipids, especially
  phosphatidylcholine, but may also include other lipids, such as egg
  phosphatidylethanolamine, so long as they are compatible with lipid
  bilayer structure. A liposome design may employ surface ligands for
  attaching to unhealthy tissue.

About cell membrane

The cell membrane (also known as the plasma membrane or cytoplasmic
  membrane) is a biological membrane that separates the interior of all
  cells from the outside environment.The cell membrane is selectively
  permeable to ions and organic molecules and controls the movement of
  substances in and out of cells. The basic function of the cell
  membrane is to protect the cell from its surroundings.
It consists of the lipid bilayer with embedded proteins. Cell
  membranes are involved in a variety of cellular processes such as cell
  adhesion, ion conductivity and cell signalling and serve as the
  attachment surface for several extracellular structures, including the
  cell wall, glycocalyx, and intracellular cytoskeleton. Cell membranes
  can be artificially reassembled.

So the major difference seems to be the presence of "embedded proteins" inside the cell membrane.


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Why are abiogenesis and evolution considered unrelated?
When a discussion about evolution comes across abiogenesis - the typical reaction is that they are unrelated (see the headline at http://www.factsnotfantasy.com/abiogenesis.php).
It seems to be that both are stochastic processes in which less ordered structures become ordered.  It seems that, in general, abiogenesis is the process of forming of life (whatever that is) whereas evolution is the process in which life would develop into more complex forms.  In other words, it seems that it's really just two phases of the same type of process and I'm wondering why they are considered as such isolated fields.

I wouldn't go so far as to say that they are entirely unrelated -- our understanding of selective processes can certainly inform our study of the origin of life -- but I would say that they are quite different projects.
One important reason is that evolutionary biologists can use phylogenetic information to reconstruct much of the history of life. For example, genetic sequencing techniques allowed us to definitively work out the evolutionary relationships among humans, chimps, and gorillas. But this approach can only allow us to back as far as the last universal common ancestor (LUCA). LUCA was presumably a DNA-based (uni-)cellular lifeform, given that these characteristcs are shared across the entire tree of life. So we have no phylogenetic information that we can leverage to reconstruct what happened to get us from a soup of organic molecules to LUCA.
Another reason is that evolutionary biology focuses on what happens to a population in which we have variation, heritability, and selection. Early in the origin of life, a structured system of heredity would not yet have arisen and so we would not see natural selection occurring in the form that we usually study it -- though there could be interesting selective dynamics in such a system.

So is the answer is that they use different tools to study the development so the sciences are different?  Eg.  Maybe astrophysics vs pool-table-physics.  Ultimately its the same physics but the types of problems they are solving are different and require different tools and specialized knowledge?  Is that the idea/direction?

Yes, that's right. And not only do we use different tools, the people doing the work are often in different departments. In addition to biologists, chemists, geologists, and atmospheric scientists play an important role in the study of life's origins.