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If during exercise the affinity of oxygen for haemoglobin is decreased, what are the general consequences for tissues?
During exercise more respiration occurs, and hence more oxygen is required.
So the oxygen dissocation curve is shifted to the right.
So at a given Oxygen partial pressure, the haemoglobin is less saturated with oxygen, i.e. haemoglobin has less affinity for oxygen.
What is confusing me is that the role of haemoglobin is to move oxygen around the body, so if it has a lower affinity for oxygen, won’t it compromise this function? Even though more oxygen is released, doesn't the haemoglobin have to carry it to all the tissues in the body? So how is this change in affinity of benefit if it reduces the oxygen subsequently available for other tissues?

Search this list for h(a)emoglobin. This sort of question has been asked before. And while you are about it, tell us what effort you made to answer this question yourself. It is well described in numerous places on the web.

I have done a google search but could only find information stating that when we need oxygen, the curve shifts to the right and Hb % Sat decreased.
What I want to know (and could not find on the web or here) is that if the point of Hb is to move oxygen around the body, wouldn't a decreased Hb affinity for oxygen reduce the oxygen parts of our body get? So wouldn't a right shift  in one way 1) make it easier for the body to absorb oxygen but in another way 2) stop Hb transporting oxygen to parts of the body that need oxygen. I.e. wouldn't these two things work against each other.
Thanks.

I have tightened up your question, spelling haemoglobin in full (avoid abbreviations for clarity and indexing, especially in titles). I have also tried to answer your question. I think it is useful to have the curve in front of you, but I could have just said that it is not a zero-sum game, but even if it were, one can change the distribution of resources without starving those with lower priority.

The only part of the body with a major effect on O2 Sat/affinity is in the muscles, where the ph is decreased. The rest of the body will be relatively unaffected, and compensatory mechanisms kick in.

It may help to consider the diagram below which shows the percentage saturation of haemoglobin with oxygen (and hence how much it takes up or releases) at the different partial pressures in different tissues. (The actual pattern — and values — depends, of course, on the blood flow to different tissues.)

In general, the curves show that at the high oxygen pressure of the lungs haemoglobin is near saturated with oxygen — Hb takes O2 up —, whereas at the lower oxygen pressure in the peripheral tissues the saturation is less — Hb releases some O2. So in normal circumstances oxygen will be gradually released to tissues as it circulates through the body. The oxygen pressure in the tissues is acting as the control valve for release.
In cases where there is a vastly increased demand for oxygen, this normal control is insufficient. The hydrogen ions in the acids produced by respiration (carbon dioxide and perhaps lactate) act as an additional control as they cause the oxygen dissociation curve of haemoglobin to change e.g. from 1 to 2 in the diagram. (The molecular mechanism of this is understood, but that is not the question.) Hence at the same oxygen pressure, more oxygen is released (cf. the percentage saturation at 1 and 2).
Does this harm tissues other than the ones producing the acid? They obviously have lower priority, but you can see there is still oxygen left at 2, and physiological mechanisms (faster heart beat etc.) will increase the blood flow in general. So it is wrong to think of this as ‘all or nothing’, but as part as a general response which alters the balance towards the tissues in greatest need.


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How do multiple replication forks function without 'colliding', and what is the benefit of this method?
I'm currently reading a little about DNA replication, and have come accross the following statement;

Replication starts from a fixed point and is bi-directional ... In Eukaryotes, there are multiple replication forks, each progressing in a bi-directional fashion.

If there is a single, long strand of DNA in a Eukaryotic cell, I see potential problems with this:
These forks involve opening up a section of double-stranded DNA, and each strand becoming a double strand in a newly synthesised piece of DNA. At some point, before any single fork has become two new double-stranded molecules, another fork could 'collide' with this, causing it to attempt to replicate the non-finished section.
Simply, how can one replication fork meet another without either exponentially increasing the number of strands being replicated?
Also, on a more general level, I would be quite interested to know the actual benefit of this, when, typically, only a single copy of the double-stranded molecule needs making.

To get to the exponentially increasing number of strands, the replication would have to be started on the already replicated strand, and not on the original strand. Replication in eukaryotes is tighly controlled and such an event is prevented by the regulation.
How can the cell prevent re-replication of the strand that is currently synthesized? By timing the steps of the replication in strict order and preventing any replication outside of that order.
Replication starts at defined origins of replication. In the G1 phase, pre replication complexes (pre-RCs) are assembled at the origins of replications. At these pre-RCs the replication can be initiated, but pre-RCs itself cannot be assembled in the later phases of the cell cycle. When the replication starts, the pre-RC is converted to a post-RC which can't initiate the replication anymore, preventing re-replication.
The benefit of multiple origins of replication is replication speed. Eukaryotic genomes can be much, much larger than those of simple bacteria. Replicating them using a single origin of replication would take a very long time.
Some further reading material:

Genomes, 2nd edition, chapter 13
Cell Cycle Regulation of DNA Replication

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Recommended sequence clustering algorithm for transcriptome data
I'm working on a project where I'm going to analyze a large amount of transcriptome data. After assembling our RNA-Seq reads into contigs using Trinity, it looks like I'm going to have about 10GB of sequences in fasta format. Since these sequences are from several hundred tissue libraries but from a single species (chicken), I'm expecting there to be a lot of redundancy, so I'd like to cluster these sequences and just use a representative sequence from each cluster as I go forward with my analysis. I see there are quite a few tools that exist to do things like this, and I'm wondering which you all would recommend. I'll be running this on a Linux machine with 64 CPU cores and ~500GB of RAM.
I started looking at USEARCH, but it seems I'm going to run into some memory issues with the free 32-bit version and as much as I clicked around on their site I couldn't figure out how much the 64-bit version costs or how to buy it.

I guess clustalw should be able to do this.. but I am not sure how to get the clusters.. May be in one of the output files.. Just check it... If you want to use multicores then you need a parallelizable tool.. i'll look up

It does sound like you have a lot of data.
I would first try Robert Edgar's other newer tool UPARSE which is faster and can handle more data using the free 32-bit version.  I think you'll mainly be limited by machine memory though, right?
Did you try CD-Hit?

Yeah, memory is going to be the limiting factor. I did just set up CD-Hit on my machine, so I'll give that a try.

cd-hit-est is probably a good option

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Which way to run BLAST?
I have a set of scaffolds from a genome assembly, and I want to align a collection of proteins from various species to it. I can do this using BLAST in two ways:

Create a BLAST database of the scaffolds, and run tblastn on it with
the proteins as the query.
Create a BLAST database of the proteins, and run blastx on it with
the scaffolds as the query.

Should both of these produce the exact same hits? Will there be any significant difference in running time between them?

Quick answer: use tblastn.
As a general rule, when comparing two datasets using BLAST, it is recommended to use the larger of the two sets as the database and the smaller as queries. The main difference is one of computational time. Blast is optimized for large databases.
You are also likely to get different hits. Blast's e-value is calculated based on the size of the database, among other parameters. Roughly, the e-value answers the question: "How many high scoring sequence pairs with X% of sequence identity and Y length would I expect to find in a database of size X by chance?". Your e-values could be artificially high if you use the protein sequences as a database. I am not sure about this, but there may also be differences in the way gap penalties are dealt with by tblastn and blastx.
That said, I would first try doing this using a tool specifically designed for the task. BLAST has no model for dealing with splicing and it is a pain to build gene models from BLAST results. To align protein sequences against genomic DNA I would use either exonerate (with the p2g model) or genewise. Both programs incorporate splicing models and will give you a decent prediction of the gene structure of your target genes. The following are extracts from each program's man page:
GENEWISE:

Genewise2 compares a protein sequence to a genomic DNA sequence,
  allowing for introns and frameshifting errors.

EXONERATE:

exonerate is a general tool for sequence comparison.
GAPPED ALIGNMENT OPTIONS
-m | --model
protein2genome
This  model  allows  alignment of a protein sequence to genomic DNA.   This is similar to
                       the protein2dna model, with the addition of modelling of introns and intron phases.  This
                       model is simliar to those used by genewise.

In general, genewise gives slightly better results but is much slower and cannot deal with multi fasta files. It is best when you know that your query protein will align against a specific nucleotide sequence.
Exonerate is fast but uses some heuristics that can give slightly worse results in some cases. Personally, I use exonerate to get my hits and then, if necessary, refine the gene model using genewise. In most cases, exonerate should be enough though.
EXAMPLES:
exonerate -m p2g -q proteins.fasta -t scaffolds.fasta > output.txt
genewise -pretty -pep -gff single_prot.fasta single_scaff.fasta > output.txt

Thanks for your response. I'll be using the BLAST results to construct a "hints" file for use with the Augustus gene prediction program, so this isn't generating my final gene model. That said, it still might be better to use one of the programs you mention.

If you want to go the BLAST way, use tblastn. I really recommend exonerate though, it knows about in-frame stop codons, splice sites, exons etc. Otherwise, you will need to filter out pseudogenes and duplications from your  BLAST hits.


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Difference between mice and rats
What is the actual biological difference between mice and rats? Are they actually the same thing with two different names depending on appearance (are they all mice for instance and we call the larger ones rats or vice versa) or is there some fundamental difference in their genetics?

Different species by definition have different body chemistry, else they could mate. However, identity on the gene level is probably similar to the man/ape difference of 98 per cent, so MOST body chemistry is identical.

To compute exactly which genes are new in one of the species vs. their ancestor, you could use orthology data from omabrowser.org

How can anyone upvote such a dreadful question? It should have been closed years ago as showing lack of any effort by the poster to answer it himself. Allowing this sort of question drags SE Biology down into the gutter!

Mice (Mus) and rats (Rattus) are definitely separate species, by whichever definition of species you choose to use. They are genetically distinct, and both genera are members of the clade Muridae, along with Acomys ("spiny mice") and Gerbillus ("gerbils").
Moreover, what we call colloquially "mice" and "rats" encompass a great deal of variation within rodents. The genus Mus is one of several subgenera with ~15 species.
A recent phylogenetic study of rodents by Blanga-Kanfi et al. (2009), revealed that Mus and Rattus are sister groups, meaning that each is the other's closest relative. The image below from the paper above shows the complete tree. Muridae is about 2/3 of the way down in blue.

True rats and mice are rodents that constitute part of the subfamily Murinae in the family Muridae. The Old World house mouse is Mus musculus, the brown rat is Rattus norvegicus, so they are members of two different genera in that family. It is estimated that they split from a common ancestor 12-24 million years ago. Just to put that in perspective, the rodent lineage (including rats and mice) and the primate lineage (apes, monkeys, humans) diverged about 80 million years ago.
You can read an NIH News Release about the rat genome here, which is my source for these divergence times.
The names 'rat' and 'mouse' are also used in the names of many other, more distantly related, rodents such as mole rats and dormice.
Added later:
Response to @rwst comment under the OP. Here is a relevant quotation from the NIH source that I cite above:

The new analysis also underscores the fact that while rats and mice look very similar to the human eye, there are significant genomic differences between the two types of rodents. For example, some aspects of genomic evolution in the rat appear to be accelerated when compared to the mouse. According to the new analysis, due to the unusually rapid expansion of selected gene families, rats possess some genes not found in the mouse, including genes involved in immunity, the production of pheromones (chemicals involved in sexual attraction), the breakdown of proteins and the detection and detoxification of chemicals.


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How did giraffes develop their rete mirabile failsafe?
Giraffes, being one of the tallest mammals in the world, have a failsafe called rete mirabile to prevent them from dying from excessive blood pressure while lowering their head.[1]
Due to their long necks, a formidable amount of blood pressure is needed (quoted from animals.about.com):

A giraffe's heart has special adaptations to enable it to pump blood up the animal's long neck to its head.
  A giraffe's heart has the formidable task of pumping blood at high enough pressure so that it can flow up the giraffe's neck to the brain.
  To accomplish this, a giraffe's heart is specially adapted.
  It can weigh up to 10 kg (22 lb) and generates twice the blood pressure of other large mammals.
  Having enough blood pressure to pump blood to the brain when the giraffe's neck is extended upward is one challenge, but when the animal lowers its head it risks injury due to excessive blood pressure.
  To counter this, giraffes have a pressure-regulating system known as the rete mirabile which restricts the amount of blood that rushes towards the brain when the giraffe lowers its head.

How did this evolve? I believe in evolution but I can't wrap my head around this. If an "overload" of blood would reach the giraffe's brain while it is, for instance, drinking water and either instantly killing the animal or severely wounding the animals mental and physical capabilities by rupturing the brain, how could a failsafe like this evolve?

According to Wikipedia, http://en.wikipedia.org/wiki/Rete_mirabile, these structures are widespread in vertebrates, and usually play a part in equilibrating two parts of the bloodstream (heat, ions). So this would simply require the adaptation of a prexisting structure to take on an additional role, with obvious selective advantage - if there is a selective advantage to having a long neck then there will also be one to changes that accommodate it.

Thank you for moving it to Biology. Im still navigating myself around StackExchange. Reading these comments they all make sense, but I feel my intention with asking this question is far too widespread and traces too far back in evolution, where it's more or less impossible to answer. Thanks for your time and input :). Question can be closed.

I think what leads to the confusion here is the assumption that the neck was evolved before the rete mirabile.  Giraffes evolved from creatures with shorter necks.  As evolution occurred nature was selecting for longer neck creatures (being able to eat more leaves) but at the same time creatures with longer necks had problems with blood pressure.
At this point this would also not be lethal because we are talking about animals with much shorter necks, just in some way disadvantageous to the animal.
So over time necks got bigger, blood pressure went up, and blood vessels developed that could better and better deal with the change of pressure. Rete mirabile also occur in other animals, so they are not a rare evolutionary phenomenon of giraffes.

its also true that since some reptiles and birds have Rete mirabile, that these short necked giraffes already had a mechanism to adjust the blood pressure rapidly.  Its not hard to imagine that theirs simply adapted to more extreme conditions as the necks got longer.  giraffes whose necks got longer without a well adapted compensation of blood pressure just didn't make it.

Thank you, this made a lot of sense! This'll make it easier to fall asleep tonight :)


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Parallel DNA double-helices with Watson–Crick base-pairing: Why do they not occur?
I know that parallel DNA helices exist and are governed by Hoogsten base pairing, but why can’t they be possible with Watson-Crick pairing? In the diagram below, if we were to flip one of the strands while keeping the other the same, it appears as though hydrogen bonding is still possible.
The only specific suggestions that I could find was because of the DNA replication process and the negative polarity of hydoxyl group on the phosphates. Moreover, after flipping one strand, the DNA nucleotides form enantiomers. Are these possible reasons, or are there others?

this question should cover it : https://biology.stackexchange.com/questions/27839/why-is-dna-antiparallel-can-it-be-parallel

I have not previously reviewed  that answer and many others but the questions stated above still remains. I would appreciate if someone could objectively answer them

Related: https://biology.stackexchange.com/questions/58156/are-there-functional-examples-of-parallel-dna-double-helices

@canadianer — I have changed the title again. Your revision ("Why isn't Watson-Crick base pairing used in parallel DNA helices?") had the falsse implication (I am sure unintended) that parallel DNA helices existed in the sense that they were reasonably widespread, or that those that had been engineered had complementary base-pairing, but of the non-WC type. My revision retains the emphasis on the lack of WC base pairing in parallel helices, but removes these implications, for the most part. Trust this is ok.

@David Yes, sounds good to me.

“The only specific suggestions that I could find was because of the DNA replication process and…”

No. The explanation can have nothing to do with DNA replication. If the structure does not exist, you can’t replicate it, if it does, Nature will evolve a mechanism. (The related SE question, mentioned by @Gilleain, asked whether it could still replicate if it were parallel, i.e. using the enzymes that have evolved for parallel DNA.)

I know that parallel DNA helices exist…

Let us clarify this first. Perhaps the most extensive parallel duplex DNA, the structure of which has been determined, is that described by Parvathy et al.. The two parallel strands of this are shown below:

The following points should be noted:

This parallel DNA (and the shorter examples that preceded it) is not a pure stretch of complementary base pairs.
It is stabilized by what the authors refer to as “CC+ clamps” at either end. One is left to conclude that without these the duplex would not form.
All the complementary base-pairs are of the type AT (actually reverse Watson–Crick base pairs). Presumably GC base-pairs would have destablized the structure.

(You can inspect this structure in three-dimensions here. Choose ‘Licorice’ style and colour ‘by chain’ and notice the non-planarity of the three base ‘pairs’ at each end.)
So although the question refers specifically to parallel DNA helices with Watson–Crick base pairs, it should be recognized that extended parallel DNA helices composed of any kind of complementary AT and GC base pairs are not found, and the question applies equally well to them.

“In the diagram if we were to flip one of the strands while keeping the other same, hydrogen bonding is still possible”

The diagram in the question is two-dimensional; DNA is three-dimensional. It is only by considering the three-dimensional structure of DNA can you approach this question.
So how would one do that? One must consider the free energy of alternative structures in the relevant millieu to determine which will occur (i.e. be more thermodynamically stable).

This will tell you whether single DNA strands with parallel sequences will form a double-stranded (ds) structure or not.
This will tell you whether ds-parallel DNA is more or less energetically stable than a ds-antiparallel DNA. Hence, even if both can form (which I doubt, without some special circumstances*) the lower thermodynamic free energy of the anti-parallel dsDNA would give organisms adopting it an evolutionary advantage.

And the answer to the question?
It seems unlikely that one single factor is responsible or it would have been pointed out in elementary text books such as Berg et al..
To answer would require a complete theoretical analysis of the structure or structures. First one would have to build a model of a proposed parallel structure that could accommodate Watson–Crick base pairs. This in itself is a problem because there are likely to be many alternative structures. Perhaps there are computer programs that can find the structure with the lowest energy. This would be calculated in the classic manner, calculating the positive contribution of hydrogen bonding (which depends on distance and angle), ionic interaction etc.*  against the negative contribution of charge and steric repulsions.
*Etc? The two-dimensional diagram fails to consider the contribution of base stacking (how could it?), which contributes to a considerable extent to the stability of nucleic acid helices, as the original cover design of Stryer’s Biochemistry is a constant reminder:

Could you please explain what you mean by 'CC+ clamps on either end”?
And what i meant was that the hydroxyl group,
Now represented by a negative Oxygen molecule in the diagram attached to the phosphorus on either end are negatively charged, which might cause them to repel and therefore to some degree constitute the formation of Antiparallel DNA

do you think the parallel dna model would continue to form hydrogen bonds or would this be disrupted,  moreover how would one calculate the free energy associated with the two dna models?

@AnamikaGhosh — 1. I have expanded my footnote to explain the CC+ clamp, which is in the paper I cited. 2. I have removed my reference to your remark about the phosphates as at is peripheral to the main argument and not worth getting bogged down in. 3. I will explain about calculating energies in a further footnote sometime this weekend. If you are impatient think about this section of Berg et al.

Thank you,  it makes a lot more sense to me now.

Glad it was of use. I learned something too. I have now added a link to a 3D view of the structure at the Protein Data Bank.


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Are RNA cleavage sites always polyadenylated?
During RNA processing (including both mRNA and non-coding RNAs), is the end of 3'UTR always polyadenylated after cleavage?
I could not find the answer to my question in the Wikipedia entry for polyadenylation.
If a recent reference could be provided, that will be great. I've done quite a bit search and hasn't found a good source yet.
Some background to this question: we are developing bioinformatics tools to predict potential cleavage sites, we need to understand this problem better in order to design a suitable algorithm

I'm not sure what you mean by "mRNA processing, including both coding and non-coding" or why you need to qualify this. Surely all you are interesting is that part of the mRNA processing that recognizes the cleavage signal AAUAAA (or variants). I have edited your question, but left this for the moment. I suggest you delete "including both coding and non-coding" unless you can clarify it.

What sort of cleavage are you talking about? Do you transcription termination?

@David, sorry for being confusing. I meant both coding and non-coding RNAs.

@Nicolai, not really, after pre-mRNA is transcribed, it will be cleaved somewhere towards the 3' end.

Then I messed your question up. I'll correct it.

This answer attempts to cover only the question of mRNA processing. It does not address the polyadenylation of non-coding RNAs.
As far as I can see from the recent review by Neve et al. (2017) cleavage and polyadenylation are tightly coupled. It is interesting, in this regard, that histones mRNAs which lack polyA tails, have a different structure, lacking the canonical AAUAAA, at their 3ʹ ends (see review by Marzluff et al.).
As distinct enzyme activities are involved in cleavage and polyadenylation, it would, I imagine, be possible (either genetically or chemically) to disrupt the protein complex responsible for polyadenylation and hence prevent it occurring (this has probably been done). However this would not be physiologically relevant.
There is an earlier review by Tian and Graber (2007) of the sequence requirements of the cleavage site which makes no distinction between cleavage and polyadenylation.
However this is not my field, so others may have additional information I have missed.

@zyxue — I think you are having trouble or typos with your negatives again. Surely you mean "It DOES seem… most are polyadenylated". Agreed.

Quote from Neve et al. (2017): "With the exception of replication-dependent histone genes, metazoan protein encoding mRNAs contain a uniform 30 end consisting of a stretch of adenosines." It does seem, at least for protein-coding mRNAs, except for histone genes, most are polyadenylated.

Thanks for the catch, @David. Do you have any lead on non-coding mRNAs, please?

Based on Table 1 from this Review paper, Strategies to Annotate and Characterize Long Noncoding RNAs: Advantages and Pitfalls
Author links open overlay panel, 2018, for non-coding RNAs, they are more often non-polyadenylated than polyadenylated.

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What is ATP and why is it said to be a source of energy?
Is ATP a molecule or a kind of energy. When I studied the active transport, it's said the ATP would release energy to change the carrier protein shape. So confused.
Thanks for your help.

Energy can't release energy, because energy is... energy. Energy has to be contained otherwise it's useless. You can't pour a handful of charged electrons in your pc can you? Plants can't store rays of sunlight in their leaves, right? They store.sun energy as glucose later to be converted into ATP to release energy. Google ATP: first line ATP wiki: called the "molecular unit of (...) intracellular energy transfer

I'm voting to close this question as off-topic because it's too trivial

Because there is so much slack usage in relation to ATP and energy, it might be worth reformulating the question title, e.g. "What is ATP and why is it said to be a source of energy?" And then reworking the question to its essentials.

ATP is adenosine 5'-triphosphate, a molecule consisting of the base adenine attached to which is attached a ribose (at its 1 position) and (at its 5 position) three phosphates, alpha-, beta- and -gamma (see edited image from Wikipedia below). The (Gibbs) free energy of hydrolysis of the phosphoanydride bonds between the gamma and beta phosphates and betweeen the alpha and beta phosphates is relatively large in terms of biological reactions. This means that coupling of the hydrolysis of ATP (usually, but not always, to ADP — adenosine 5'-diphosphate) to a reaction that is energetically unfavourable can often produce an overall reaction that is energetically favourabe (has an overall negative free energy change). Enzymes have evolved to catalyse such coupled reactions involving ATP.
Although ATP is often referred to as having ‘energy-rich bonds’ this is not the best way of thinking of things. First, and perhaps most important, you cannot think of energy in abstract, and even referring to ‘breaking a bond’ is insufficient. One is talking about free energy change which must relate to a specific reaction, in this case hydrolysis:
ATP + H2O → ADP + PO43– or less frequently ATP + H2O → AMP + pyrophosphate
Second the free energy change is only ‘high’ in relation to cellular reactions. Third the energy is only of any use if it can be coupled to these reactions (or processes like active cation transport).
It is perhaps better to refer to ATP as having a ‘high phosphate group transfer potential’.
The coupling of the hydrolysis of ATP to mechanical processes like muscle contraction or the change of shape of transporters (if that is what happens) is more complex, but obeys essentially the same principles. The  ATP hydrolysis reaction with its favourable negative change in free energy is coupled to the  mechanical process with its unfavourable positive free energy change.
Further Information

ATP and Free Energy: https://www.ncbi.nlm.nih.gov/books/NBK9903/#A295
‘High Energy Phosphate’: https://en.wikipedia.org/wiki/High-energy_phosphate
ATP and Cation Transport: https://www.ncbi.nlm.nih.gov/books/NBK9847/


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How is it determined which parts of an mRNA precursor are to be spliced?
According to my textbook, the same pre-mRNA sequence can get spliced in multiple different ways. But how is this regulated by the cell? How are the introns and exons to be spliced determined?

Welcome to SE Biology. Please finish the [Tour] and then How to ask good questions.  You will see there "Have you thoroughly searched for an answer before asking your question?… Tell us what you found and why it didn’t meet your needs. This demonstrates that you’ve taken the time to try to help yourself…" The term you should search for is "RNA Splicing". You will see related questions to the right here, a section in Wikipedia, and sections in Berg, Lodish and Alberts on NCBI Bookshelf.

Oh, and cells don't "know" anything. Acceptable scientific terminology would be "How is it determined which parts of a mRNA precursor are spliced?", "What is the mechanism by which a mRNA precursor is spliced at specific positions?" or "How are the splice sites recognized on mRNA precursors?". Precision in scientific communication is important. Sloppy speech leads to sloppy thinking.

As the textbooks available in NCBI Bookshelf are often older editions and the field of "alternative splicing" has advanced rapidly, try to find the 9th Edition of Lodish (2021) or the 6th Edition of Alberts (2017).

@Armand In an ideal world yes. But these are freely available and appropriate to a question at a completely naive level.

Your question is a good one, and has given rise to decades of intensive research, which continues today. The short answer is that many factors are involved, ranging from sequences within the gene up to chromatin-level changes.
De Conti et al. in their review "Exon and intron definition in pre-mRNA splicing" (2012 DOI: 10.1002/wrna.1140) note:

Most importantly, these influences act across several levels of
complexity starting from the relatively simple interaction between two
consensus 5' and 3' splice sites to much more complex factors: such as
the interplay between silencer or enhancer sequences, transcriptional
processivity, genomic milieu, nucleosome positioning, and histone
modifications at the chromatin level. Depending on local contexts, all
these factors will act either antagonistically or synergistically to
decide the exon/intron fate of any given RNA sequence.

In the big-picture view, there are two types of intron-processing complexes or "spliceosomes" found in most metazoan cells.  Akinyi and Frilander ("At the Intersection of Major and Minor Spliceosomes: Crosstalk Mechanisms and Their Impact on Gene Expression" 2021  DOI: 10.3389/fgene.2021.700744 ) summarize:

The majority of introns (more than 99.5% in humans) are recognized and
excised by the major spliceosome, which utilizes relatively poorly
conserved sequence elements at the 5' and 3' ends of the intron that
are used for intron recognition and in subsequent catalysis. In
contrast, the minor spliceosome targets a rare group of introns
(approximately 0.5% in humans) with highly conserved sequences at the
5' and 3' ends of the intron.

Finally, it now seems clear that intron/exon structure developed at roughly the same time as eukaryotic cells.
Rogozin et al. ("Origin and evolution of spliceosomal introns" 2012 DOI: 10.1186/1745-6150-7-11 ) write:

Reconstructions of intron gain and loss using the growing collection
of genomes of diverse eukaryotes and increasingly advanced
probabilistic models convincingly show that the LECA (Last Eukaryotic Common Ancestor) and the ancestors
of each eukaryotic supergroup had intron-rich genes ...

There is no indication that any prokaryote has ever possessed a
spliceosome or introns in protein-coding genes, other than relatively
rare mobile self-splicing introns.

Here's a review of the molecular machinery at work: "The nuts and bolts of the endogenous spliceosome" Sperling 2017 DOI: 10.1002/wrna.1377


text:
How does Heat Fixing make cells stick to a slide?
Regarding Gram Straining, my college instructor told us how we pass the slide with the bacteria on a bunsen burner 3-4 times and it fixes the bacteria so that they don't get washed away with water. How does the heat fix the bacteria that on the slide?

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Have you ever put a peice of meat into a searing hot pan and had it stick? That piece of meat is thick, yet it still sticks, Imagine if it were only a few cells thick, What are the odds it would wash off with water?

I haven't done that but yeah I have seen the meat stick to the pan but why does that happen? Why does the meat or the cells stick to the surface because of heat? What is the science behind it?

It's because meat and skin and cells are made of (not exclusively but enough) protein, and heat denatures protein.

So why does it stick because of the denaturing of the protein?

I grasped this concept from bob1, a notable member of this site , that the term heat fixation is misleading, as heat is not what actually fixes cells in this method, it's dryness that does. In other words, anything that will get these cells to dry will fix them.
I add that generally, the actual culmination for cell fixation resides in denaturing and precipitating proteins. Drying does that. So does methanol.
Now you have two options:
1- Drying: The most reliable way to do that is air-drying, that is, leaving the slide anywhere for atleast 20 minutes or 30 minutes to be sure.
2- Methanol fixation
Heat fixation, or to say it correctly dry fixation by direct heat, is a bad method because you can easily pass the endpoint and the result of doing so is disastrous [*].
--
[*] https://pubmed.ncbi.nlm.nih.gov/6201316/


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Is being able to interbreed and produce fertile offspring a transitive relation in biology?
Being able to interbreed and produce fertile offspring is one criterion to decide whether two populations are of different species.
Are there 3 populations A, B, C such that A and B are able to interbreed and produce fertile offspring, B and C are able to interbreed and produce fertile offspring however A and C are not able to interbreed and do not produce fertile offspring?

@worldsmithhelper: Would you be interested in the general answer on populations or in an answer about species?

If there exists such populations A, B, C examples with references would be awesome. If there are multiple "reason or mechanisms" for such tripplets of populations emerging examples of each mechanism with some elaboration on the mechanism would be appreciated. If there exists species tripplets A, B, C (and since every species is a population) they are welcome to. It doesn't have to be exactly triplets either quintuples or a continous spatially distributed population which has this property also works. If there is a strong reason or argument why this can't work that would also be accepted.

A useful example may be modern dogs, you have the chihuahua-great Dane problem, they can't interbreed without human intervention. and that is just breeds of the same species.

The ring species conundrum
As commented above, in essence this is the classic case study of ring species, and reading up on it will completely answer your question. A case of ring species is visualizable geographically (area A, area B, area C, and 'variant species' graduating across).
'Transitive', jargon and the idea of transition
Sure, something's transitive if A is B, and B is C, and it follows that A is C. But species are not transitive sets (of numbers). It's a bit along the lines of 'mixing'. Say, by analogy, if water dissolves soap, and soap dissolves fat, it does not mean that water dissolves fat. I wouldn't use mathematical terminology in biology (i.e. I would also not call species intransitive or nontransitive, it would not be helpful) but I would rather focus on the concept and word "transition". Lineages evolve and diverge gradually, some remain extant and co-exist with- and sometimes without interbreeding. I think lineages you can talk about in a very robust manner in the long term. The 'species' category is more about 'binning', deciding which section or degree of branching of the lineage you want to consider a unit.
Imagine the concept phylogenetically
Extant (currently living) canines are a nice example. Those similar can interbreed naturally, those dissimilar cannot realistically or even physically or genetically interbreed. Chihuahuas and wolfhounds or Great Danes could be construed as different species with our classical definition of species, because they truly do not interbreed. Yet they are widely and scientifically today considered the same species! You can surmise that there is difficulty with this classical concept of using 'species', when used stringently and in a strictly categorical fashion... let's consider it from another point of view...
Imagine the concept though time
If one's ancestors 5 generations back could interbreed with ancestors 10 generations ago, we could 'define' them as a species. Perhaps even those 5 and 1,000 generations back. What about 10,000? What about 100,000? 100,000,000,000? You see, every generation can interbreed with the next, yet at some point we choose to categorize them as different species. You have to understand that we define biological species not because there is such a real thing as a species boundary, but only because it helps us think about things by chunking them arbitrarily together. The concept of species is useful, but not objectively a feature in reality.
I would also refer you to my previous answer on what the definition of a species is and why it's always been problematic. I think that will help with a more complete understanding.

If you want to give a short summary what one is supposed to get from ring species i can accept the answer. As is the answer doesn't really answer the question but points to resources which do.

@worldsmithhelper An example may be to look up the classic example the Larus gulls. what we learned is these classical species definitions fall apart in light of modern genetics. they are useful tools of simplification not accurate representations of reality.

@worldsmithhelper I believe I've answered your question. Can elaborate when I find some time to spare... but as mentioned, ring species case studies are just an iteration (manifestation) of your abstract question. You asked for an example. There are many to find in ring species, and entire books have been written on this motif. Consider my mentioning ring species as simply grounding the question prior to expanding your understanding of the species concept. I rather think it more suitable to address your (mis)conception that there is such an immutable, exclusive identity such as 'species'!


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Why do cells use microRNA to break down mRNA, instead of not transcribing it in the first place?
As I understand it, microRNAs are used to ensure that certain genes are only expressed when needed. The way this apparently works is that when the translation products of an mRNA are not required the appropriate microRNA is transcribed to bind to the mRNA and initiate its nucleolytic degradation.
My question is if the cell can detect that the product of a specific mRNA is not required why is the mRNA transcribed it all, rather than synthesizing it and then synthesizing another RNA to silence it?

Hi Sam. I rolled back your recent edit, but I understand your frustration. Yours is an interesting question, though, as it stands, it is practically impossible to answer. If you reduce the scope of your question, you may find someone willing to take a crack at it. For instance, instead of asking why microRNAs exist (redundancy?), perhaps you can ask whether microRNA regulation is energetically beneficial from the cellular perspective, relative to control at the levels of transcription (TF abundance and binding) or translation.

@acvill: I disagree. It is not impossible to answer. miRNAs allow a cell to rapidly remove any present mRNA in order to react quickly. Furthermore, every mRNA is subject to constant production/degradation (RNA Homeostasis, Pelkmans 2022). This question is about RNA biochemistry. This does not contain an answer.

@markur your comment addresses how miRNAs help maintain mRNA homeostasis. The question asks why miRNAs evolved as a control mechanism. We can speculate, but, generally, it’s very difficult to know why a particular trait or pathway evolved alongside / in lieu of another.

@markur if you believe the question should be reopened, feel free to submit an edit.

@acvill ok cool, I submitted an edit, let me know if I did something wrong. And sure, I get why one might consider this question is related to "traits". However, I feel it's unfair to depict this question as speculative, considered that there is just so much knowledge about how and why RNAs are produced and regulated and degraded etc.

@acvill — I disagree. The question is from a naive user ("I am learning" or something of the sort) who seems not to realize that if you light a candle and finish the game you may want to snuff the candle out as well as not lighting another. Of course the question of why one mechanism rather than another for a specific gene is speculative and has to be considered on a case by case basis, but I think that can be mentioned, with examples of other regulatory mechanisms. There is also the point of circuits and oscillations with multiple regulatory controls (that I do not understand). Try my edit.

@David that's a good edit. I'll vote to reopen.

The key differences are:

miRNA act very quickly (hours, day). Transcriptional repression stops production, but doesn‘t remove the gene‘s signal since the mRNA is still there.
one miRNA can target multiple (even hundreds of) different transcripts  coming from different genomic loci, causing significant changes to the transcriptome at once. That‘s needed for differentiation processes (see let-7: Balzeau 2017). Transcriptional repression can‘t handle that, since that would impose more extensive requirements on promoters/enhancers. (Ni & Leng 2015)
miRNA evolved from an anti-viral system (RNA interference) that degrades viral dsRNA. Its machinery is multifunctional.
miRNA can be transported between cells within extracellular vesicles. That way, intercellular communication causes quick changes to transcriptomes. Transcriptional repressors can‘t do that as easily, since they‘re localized to the nucleus and not the cytosol.

Simple Answer
Switch On: To start expressing a protein-coding gene — synthesizing its product — you have at some stage to synthesize its mRNA — transcribe it.
Switch Off: To stop expressing a protein-coding gene it makes sense to stop making more RNA, as the poster suggests. But that may not be enough! Many eukaryotic mRNAs have half-lives ranging from hours to days, so that merely stopping transcription will not immediately stop the protein being produced. If it is important to stop synthesis immediately, something else is required. Nucleolytic degradation of the mRNA initiated by microRNAs is one way to do this.
More than one way to kill a cat
Why is this not more widespread? The answer is that this is only one of a variety of means to regulate gene expression. Others include having mRNAs of shorter half-life (as in bacteria), controlling mRNA translation, inactivation of the protein (if it is an enzyme) or degrading the product by proteolysis. Which method is employed depends on evolutionary chance, the nature of the system, whether it is advantageous to be able to resume activity quickly etc. So systems regulated by microRNA need to be considered on a case-by-case basis.
And although I am not competent to write on this (additions solicited) I am led to believe that mathematical modelling shows that the existence of a variety of regulatory mechanisms can allow a smoother and more buffered response to a variety of stimuli.


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Aligning two PDB structures with different numbers of atoms
What options do I have to align two PDB-files of ribosomes but with different number of atoms? I need to do the alignment using selection "name CA or name P", because the ribosome has both protein and RNA.
From my previous work I learned that PyMol can do alignment where it doesn't matter if the number of atoms is different, but there is problem because PyMol can only do the alignment using CA atoms, and thus it ignores my "name P" from rRNA.
I also tried to align the structures in VMD using RMSD Calculator but there needs to be same number of atoms in both selections. I also tried MDAnalysis code but there is also the problem that the selection doesn't have the same number of atoms.
Are there any suggestions on how to perform such an alignment? The best option seems to be PyMol (as it works with a different number of atoms in the two selections), but how do I incorporate the RNA into the alignment?

You may have more luck on SE Bioinformatics. (Oh, and amount of sugar, number of lumps.)

I use ChimeraX for structural superposition and it may work for your needs. See this command specifically. It also has a GUI.

Does this answer your question? How to perform a DNA structural alignment in pymol

When encountering that problem for single pdb files I often default to using the MultiSeq tool in VMD. This pairs sequence information and structural information to create very good alignments. MultiSeq can also align RNA.
If you require to do this over a trajectory, I would start by doing an alignment with MultiSeq and from this alignment identify residue-residue correspondences. Ignore gaps in the sequence alignment and align the backbone atoms of all other residues. This ensures that the number of atoms is identical in both selection and that you can use the "meausure fit" command in VMD.
In VMD you need to make sure that the selected atoms are in the correct order. Assume that you have two sequences that align like this:
AAAA---AAAA
AAAAEEEAAAA

then you can run (in VMD):
set idA [mol new MoleculeA.pdb]
set selA [atomselect $idA "backbone and resid 1 to 8"]
set idB [mol new MoleculeB.pdb]
set selB [atomselect \\\$idB"backbone and (resid 1 to 4 or resid 8 to 12)"]
\\\$selB move [measure fit \\\$selA \\\$selB]

Trajectories are then done similarly by moving through with animate goto \\\$frame in between.
When using the MDAnalysis python library you can make use of a selection dictionary for alignment. The select option of MDAnalysis.analysis.align.AlignTraj can take in a dictionary like this:
{'mobile':"resid 1-8", 'reference':"resid 1-4 or resid 8-12"}


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Do monoecious plants have bisexual flowers?
I used to think that monoecious plants have male (unisexual) flowers and female (unisexual) flowers on the same plant but on different locations. But recently I learnt that monoecious plants also have bisexual flowers,  which means the male part and the female part in the same flower.
Thus, I am confused. Can someone clarify?

Welcome to Biology StackExchange. Please, read some basics about the terminology (for example Wikipedia page on plant reproductive morhpology), then let us know if you still have any misunderstandings by editing your question.

You are correct that monoecious describes plants where the male and female structures (cones or flowers) are on the same plant but in separate locations. Plants that produce hermaphrodite flowers together with either female or male flowers, are termed gynomonoecious or andromonoecious, respectively. A plant with separate male, female, and hermaphrodite flowers is trimonoecious.
Monoecy is not to be confused with monoicy. In monoicy, both gametes, sperm and egg, are produced by the gametophyte (e.g., some plants with gametophyte-dominant life cycles [bryophytes]).

Monoecious plants have both female and male flowers in the same plant. They can be male flowers, female flowers or a mixture of the two in the same plant.


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Does Mitochondrial Eve existence suggest genetic fitness, and what evolutionary developments map to her time period?
I am not sure of the size of the population at the time of Mitochondrial Eve, but I assume it must have been reasonably large.  It seems to me that without bias, each female at that time should have an equal number of descendants. It seems very unlikely that every other bloodline would die out unless Mitochondrial Eve's descendants had an evolutionary advantage.
Is it commonly accepted that Mitochondrial Eve's descendants have an evolutionary advantage?  If so, what advantages is ascribed to her descendants?

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There's an illustration here of the kind of way things might pan out in the absence of selection. One certainly oughtn't to expect every girl born to a given generation to have even a roughly equal no. descendants through the female line thousands of years later.

Please see the following related answers:

What is a Mitochondrial Eve and Y-chromosomal Adam
Does mitochondrial eve have to exist?
Is it tautological that all living humans descended from a single male and single female human ancestor?

Because mitochondrial lineages that provide a selection advantage are more likely to spread in a population, Mitochondrial Eve (ME) is more likely to have belonged to such a lineage. However, there is no real reason to suspect that ME in particular, or her descendants, had any special evolutionary advantage over other humans existing at the same time.
The identification of Mitochondrial Eve—the most recent mitochondrial ancestor of all living humans—changes over time as mitochondrial lineages in a population go extinct. When this happens, the assignment of ME jumps ahead in time to the most recent ancestor of the remaining lineages.
Extinction of a mitochondrial lineage can be entirely random (though selection helps), and is a consequence of reproduction in a finite population. The likelihood of lineage extinction is negatively correlated with it's proportion in the population. In a population without selection, each member wouldn't have an equal number of descendants, they would an equal likelihood of having some number of descendants (e.g., their number of offspring would be drawn from the same distribution). Under this scenario, and with a finite population, eventually all lineages except one will go extinct.*
All we know about any particular ME is that she was female, and had at least two daughters who themselves each had at least one daughter.
This simply follows from the definition of ME.
We have good evidence that the current ME lived about 150,000 years ago, meaning we can also be confident that she was an anatomically modern human.
Other than those facts, the current ME is anonymous, and we know little about the total population of human mitochondria at the time she was alive.
While significant beneficial mitochondrial mutations occurred sometime before ME, and some may have appeared for a subset of existing mitochondria, it's unlikely that ME herself was the origin of any functionally important mutations.
So, beyond the general statements that mutation and selection occur in mitochondria, and that ME was a member of the successful lineage who had some daughters, there's nothing particularly special or unusual about her.

*The lineage that remains is said to be "fixed" in the population; the chance of this is equal to that lineage's starting proportion of the population. Note that other mutations can occur in that lineage during the process of it becoming fixed, so that all offspring are part of that lineage, but don't have identical DNA.


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Why are there so few full-length antibody structures?
I’m a student in the Biochemical Engineering field and the professor at the department just told us in a lecture that if we want to use a full-antibody structure for simulation purposes there aren’t very many of them. He suggested that we start with 1hzh.pdb.
So I wondered whether he was correct and, if so, why there wasn’t anyone using crystallisation or NMR to look into the structures of the antibody drugs that have come onto the market. Perhaps it costs too much and it’s very time-consuming? But, even so, I imagine that it would still be worthwhile.

You have received three answers to your question and have had enough time to consider whether you find any one of them helpful and convincing. If so, you should accept that question. If not, you might at least thank those who took the time and trouble to answer.

Apologize for the delay. Thanks for your time answering the question and providing all the comments. Really appreciate all of your opinions.

The more flexible a molecule, the more difficult it is to get a crystallization that actually tells you something about the molecule's free-phase arrangement/behavior. Basically (the best) crystallography requires you get a molecule to grow (crystals) in the same conformation.
The hinge in IgG1 for instance appears to be able to rotate from 0 to 180 degrees (although range may be more limited in actual molecules, depending on the "bulk" of what's attached to the hinge). If you somehow manage to grow a crystal of a full IgG you'll just get a snapshot of that at one angle. (That 2011 paper says there was still a single such image for a full-length [human] IgG1 for instance--the one binding HIV (IgG1 b12) found in your 1HZH file.)
According to a 2018 review only 4 full structures of IgG antibodies had been determined; by PDB entry with year of paper publication:

1IGT [1997] -- "a mouse IgG2 with 3 hinge disulfide (SS) bonds, while human IgG2 has 4 SS bonds"
1IGY [1998] -- a mouse IgG1 with 2 SS bonds
1HZH [2001] -- a human IgG1 with 2 SS bonds
5DK3 [2015] -- a human IgG4; "the hinge SS was more stabilized due to the conformational alteration of S228P mutation"

Of these, only the last one, pembrolizumab, is used therapeutically, as far as I know, but the first one, was (interstingly) a [proposed] veterinary product at one point (Mab231--against canine lymphoma); the USDA suspended its license after it failed in larger trials. The 2nd one is an antibody against phentobarbital. The 3rd/HIV one (1HZH = IgG1 b12) is not the one that's been (recently) approved for treatment  as Ibalizumab.
The first of these papers (1997) notes some earlier attempts at full structure crystallography; mostly successful in special cases where there was reduced hinge mobility:

Other intact antibody structures have been studied by X-ray
crystallography (Silverton et al., 1977; Guddat et al., 1993;
Marquart et al., 1980). In two myeloma proteins, the flexible
hinge regions connecting Fab and Fc segments were deleted
(Silverton et al., 1977; Guddat et al., 1993). The molecules
were structurally restrained and, perhaps for this reason,
appeared as compact T-shapes, the angle between Fabs close
to 180°. A third antibody, Kol, had an intact hinge, but the
Fc was so disordered that it was not possible to orient it
with respect to the Fabs (Marquart et al., 1980). The two
Fabs and a portion of the hinge (upper and core) were,
however, visualized.

The first two [fully successful] papers (1997-1998) came from the same lab/group. As I'm not expert in this area (or even in biochemsitry) it's hard for me say what was the breakthrough that enabled the full structures IgG crystal analysis in the late 1990s; the papers aren't incredibly explicit on that. There was certainly a heavy amount of computation involved on the X-ray diffraction data, conducted on a Cray C-90 supercomputer at that time; mentioned in these late 1990s papers. And the diffraction experiments were not conducted in the university where the authors were employed but at the Stanford Synchrotron Radiation
Laboratory (SSRL) and Brookhaven National Synchrotron Laboratory, respectively; almost certainly because they used the large synchrotrons available at these labs, as opposed to smaller X-ray sources. There are entire papers on the subtelties of cryportection needed in order to leverage high-energy X-ray sources.
The 2001 short paper in Science on IgG1 b12 is actually devoid of much method details, but the same (Scripps) group has published a longer paper in 2002 in JMB; there they say they (also) ran their diffraction at SSRL (beamline 7-1). No details on computational resources though.
The 2015 paper on IgG4 acknowledges the Canadian Light Source where the diffraction was conducted
on beamline 08ID-1 with synchrotron radiation. Interestingly, this paper also used TROSY (NMR) to confirm packing details and 1D NMR to compare hinge behavior in solution of a serine-to-proline replacement in the hinge (more on NMR below).
The 1997 and (to a lesser extent) the 2015 paper have most details on the computations involved (well, in this group of 4 papers). Basically prior Fc and Fab crystal diffraction "signatures" (ideally for the same antibody) are highly desirable and the software basically does a search trying to locate them in the larger "picture". But this can fail and manual hints based on parts of Fc/Fab (e.g. from similar but not the same antibody) may have to be entered to guide the search etc.
The 2002 paper has some hints why the automated search can fail (beyond the hinge problem) even when the Fab's structure has been previously analyzed separately; when the whole antibody is crystallized asymmetries are observed:

Importantly, all three of these intact antibodies
crystallize with one whole IgG molecule per asymmetric
unit, even though their respective space
groups and crystallization conditions vary. Thus,
although the two halves of the antibody are identical
in sequence, they are not identical in structure.

A (single) crystal structure will not--in itself--let you experimentally verify how much hinge freedom there is. Tomography techniques such as IPET are more sensible for the latter. Resolution is (much) lower, but if just want to capture the angles available in the hinge with something attached, it's far less time consuming. Feed the results into a targeted molecular dynamics (TMD) package together with the crystal structure of Fab & Fc, and you get something like this

As for [3D] NMR (which you also suggested), it cannot be easily used because of the too greater size of full-length antibodies (IgG: 145-160 kDa) vs 40 kDa typical limit for NMR. Basically with 3D NMR, the bigger the molecule, the "blurrier" the image your're going to get. While Wikipedia mentions a couple of proposals/experiments for larger molecules, it seems those didn't really take off in everyday practice.
There are actually some papers that have done spectroscopy NMR on full-length antibodies, but present the results with caveats like:

It should be noted that mAb2 used in this study [...] is an example of an intrinsically stable and soluble antibody. Despite this, at a very high mAb2 concentration the measurable NMR parameters registered quite significant differences as solvent conditions were varied, highlighting the inherent sensitivity of this NMR technique. It can be anticipated that other, less stable mAbs, which require more careful formulation to achieve satisfactory solubility and stability profile, would show even greater variation in NMR measurables.

There are also several papers e.g. Marino et al. (2017),
Brinson et al. (2019) on 2D NMR on MAb, but again for the purpose of determining the higher-order structure (in solution); although the resolution may be a bit better than IPET (but still below crystallography), it requires more complex math.

The methodology for the Science paper is in the Acta Cryst. D paper I discuss in my answer, and which you might have cross-referenced. I have upvoted your answer because it deals predominantly with the fact that the hinge region is flexible and thus there are a number of structures, and also because it reviews the 21st century literature. But without my own answer, the way you start would be incomprehensible to most and especially the poster. An initial statement that there are only a few full length structures and this is because of the flexibility would improve your answer no end.

There IS a problem!
In a previous version of this answer I focussed on various historical, technical, goal-related and commercial reasons for the predominance of structures of antibody fragments (Fab and Fc) rather than complete immunoglobulins (two copies of heavy and light chains) — the “full-antibody structures” of the question. I retain this as an appendix as I think it still of interest, however I had missed the main reason.
The main reason can be found in the two papers on 1HZH — the anti-HIV antibody mentioned by the poster. In a nutshell it is:

Full length antibodies have regions that convey functional flexibility, resulting in a variety of conformational forms in the same pure protein.

To quote from the paper describing the crystallization:

The Fab and Fc domains are connected by hinge regions of exceptional flexibility that facilitate changes in shape for bivalent attachment to antigen and for effector interaction. Electron microscopy of rabbit and mouse IgG has provided evidence for flexibility and arm rotation at the Fc–Fab and Fab–Fab interfaces, most of which is associated with the central hinge region.
The inherent molecular flexibility has complicated crystallization of intact antibodies.

And lest there be any doubt about the relative numbers:

While well over 200 structures of antibody fragments, mainly Fab and Fab0, have been determined [in the year 2000], crystals of intact antibodies have only been reported eight times… Only Dob, Mcg, Kol, Mab231 and Mab61.1.3 have yielded structures or partial structures.

And the paper points out the limitations of even these structures:

These early results suggested that for antibodies with normal hinges the relative placement of the Fc with respect to the Fab arms is not fixed and is free to assume a wide range of configurations.

Solving the problem
The general approach adopted by the authors is summarized in their statement:

Nevertheless, a well ordered antibody crystal can be obtained if a single conformer is incorporated into the crystal lattice owing to stabilization by crystal contacts. In this manner, a single ‘snapshot’ of an antibody structure can be obtained from the plethora of possible conformers.

Achieving this was far from simple — as far as a non-expert can judge from reading their full account, and the fact that the details of their achievement was regarded as justifying publication in the top journal, Science the following year. I reproduce below an image showing what they refer to as

a “snapshot” of the broad range of conformations available in solution.

where the hinge regions are marked.

Reflection: Utility of full-length high-resolution structures
Obtaining a high-resolution full-length immunoglobulin structure is obviously important in itself, but as the answer from @Fizz documents, there had been only one other subsequent structure of this type by the time of a review in 2018. Why is this? Granted it is intrinsically difficult, but one the basis of the difficulty — the range of different structures caused by the hinge flexibility — is also the answer. No one specific structure can be regarded as definitive, so that, as the other answer illustrates, lower resolution images of a range of structures became of greater interest, and these can be related to the high-resolution full-length structures.
Appendix: Minor reasons (from my original answer)
Historically, a fragment containing the constant domain of immunoglobulins could be crystallized from polyclonal antibodies because it was identical for antibodies of different specificities (within a class such as IgG), whereas the different variable regions prevented crystalization. One had a mixture of molecules. It was for this reason the abbreviation Fc arose — it stands for fragment crystallizable. region.
Polyclonal antibodies were available from tumours before artificial means of generating them arose, but the point of interest was the antibody-binding site, so that the Fab fragment — which was easy to generate — would serve the purpose. It is much easier to crystallize and analyse such fragments than the whole immunoglobulin, so that is why they were (and are used).
Finally, one studies the areas of immunoglobulins that are the focus of your scientific interest (and for which you can convince grant authorities are worth funding). For example, if you are interested in interaction with antigen, you solve the structure of the Fab region; if you are interested in the interaction of the constant region with other molecules (or the difference between different classes) you solve the structure of  the Fc region; and only if you are interested in a problem like the relative orientation of the different regions under particular situations do  you make the effort required to solve the structure of whole antibody.

There are thousands of structures in the PDB of neutralizing antibodies against all sorts of viruses using all sorts of methods (NMR,x-ray,electron microscopy) as complex or stand alone. I guess your professor has certain requirements that are rarely met, e.g. specifically anti-HIV-1 IGG of certain quality; then he/she only found one structure that suffices.

What search on PDB do you use that enables you to say with certainty there are thousands of compelete Ab structures?

I didn't say that.

You said there are thousands of structures. Either justify the statement or edit it. But even if you edit it to, say, “quite a few”, I would expect you to supply some examples. The principle for answers on this list is that they should be supported by evidence.

I suspect now that you may have skimmed the question and not realized the emphasis was on the structure of the whole antibody, which is quite clear if you read the papers describing the motivation for the work on 2HZH. If this is the case you may wish to consider whether to withdraw your answer.

The OP wondered "why there wasn't anyone using crystallisation or NMR to look into the structures of the antibody drugs coming into market so far". It is most important to clarify this misconception; ABs are heavily studied (source: PDB). I checked the mentioned AB and saw that it was an anti-HIV full IGG, but the actual question does NOT state that it has to be a full AB! You edited the OPs question to put emphasis on this aspect just so that it fits your answer. Most simulations are done on protein fragments anyways. It IS the Professors choice to take "full" AB!

The title of the original question started "Why are there so few full-length antibody…" That is quite clear and I did not at any time alter that. I put the emphasis in the actual question because many new posters do not realize that it is best to repeat the key points in the body of the question — it should stand alone. It is also easy when answering to miss something in the title — I've done it myself — especially if one is answering on a phone, but there is no doubt that was what the question was about, and looking up the literature on 1hzh makes that clear.


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How does NaF protect G proteins from denaturation?
Below is presented Figure 4 from the 1977 paper of Ross and Gilman, which provided evidence for the existence of G proteins:

The protocol (and rationale) is as follows:

Wild-type cell membranes was preincubated at 37˚C for 30min. (This causes loss of adenyl cylase activity, attributed to dissociation from another component — G protein — essential for its activity.)
Gpp(NH)p was then added — with a no-addition control — and the membranes further incubated at 50°C for the times shown. (The higher temperature denatures the second component — G protein —but not the adenyl cyclase. Gpp(NH)p had previously been shown to activate adenyl cyclase and was required to assay activity.)
The extracts were chilled and mixed with adenyl cyclase-depleted membranes to provide the second component. Adenyl cyclase assays were then carried out with Gpp(NH)p or NaF (which was also known to stimulate adenyl cyclase).

When incubation was performed in the absence of Gpp(NH)p, and then stimulated with Gpp(NH)p, much of the G protein denatured quickly during incubation, decreasing AC activity
When incubation was performed in the presence of Gpp(NH)p, and then stimulated with Gpp(NH)p, the G protein showed increased thermal stability, denaturing slower during incubation and decreasing AC activity to a smaller extent
When incubation was performed without Gpp(NH)p, and stimulated with fluoride, the G proteins showed similar activity to the sample stabilised with Gpp(NH)p, despite no Gpp being present during incubation.

How is the presence of fluoride ion seemingly able to reverse the denaturation of the G protein? How does it allow a level of activity similar to the Gpp(NH)p-stabilised G protein, despite the fact that the G protein was not stabilised during incubation?

Welcome to SE Biology. I have edited the first part of your question, correcting the order of authors, modulating the statement of its significance, and describing the experiment and its rationale. I think your bulleted interpretation is incorrect, but I have retained it in order to present an alternative in my answer.

Could you tell me why you think my bulleted interpretation is incorrect?

I am composing an answer — be patient. I am having to read and re-read the original paper and this is taking time.

The question is whether the authors are really using open circles for two conditions — membranes incubated with and without Gpp(NH)p but assayed in the presence of NaF. It beggars belief. But the text suggests that this is so, contrasting half-lives of 8min and 2min for NaF and Gpp(NH)p with unpreincubated membranes. Not sure you are going to get an answer now. I was attracted by the mechanism of stabilization at the protein level, which is actuall through aluminium fluoride.


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How can the directionality of a protein structure be defined?
For a DNA molecule, you can define directionality using the convention of a 5'-3' direction on the Sense strand. However, using an N to C convention for a protein doesn't work since the ends may be on the same side and if the protein is unstructured then the N to C direction will change. I'm asking the question from the perspective of addressing PPIs. If I have two proteins that interact with each other, how do you quantitatively describe the relationship of the two proteins with respect to one another. We have formal ways to describing this using domains and residues but not for quaternary structures.
How would you mathematically define "up" for a protein structure?
I would imagine that using RDCs would be able to make some progress into this problem. At the moment it doesn't seem as if there is any convention in the structural biophysics community.

I am afraid that won't be that easy. One way I can think of is by finding the net dipole moment and making that as the axis. But I think PPIs are usually not in that global scale.


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What is the appropriate method to send a strain?
We are planning to send an ecoli strain to another lab. What is the appropriate way to do so. No MTA is required but the options seem to be using filter paper or sending a glycerol stock on dry ice.

Is the lab in the same country? I am asking because international (and more so intercontinental) shipping on dry ice can be a major pain.

Good for you (I can tell you, sending samples on dry ice from Europe to Australia did quickly turn into a bureaucracy nightmare! :D)

I believe Addgene send strains as bacterial stabs.
This is the protocol from Qiagen.

E. coli strains can also be stored for up to 1 year as stabs in soft
  agar. Stab cultures are used to transport or send bacterial strains to
  other labs. Prepare stab cultures as follows:

Prepare and autoclave LB agar (standard LB medium containing 0.7% agar) as described in the last issue of QIAGEN News (1).
Cool the LB agar to below 50°C (when you can hold it comfortably) and add the appropriate antibiotic(s). While the agar is still liquid,
  add 1 ml agar to a 2-ml screw-cap vial under sterile conditions, then
  leave to solidify.

Vials of agar can be prepared in batches and stored at room
  temperature until required.

Using a sterile straight wire, pick a single colony from a freshly streaked plate and stab it deep down into the soft agar several times
  (Figure 1).

￼￼￼￼￼￼￼￼￼4. Incubate the vial at 37°C for 8–12 h leaving the cap
  slightly loose.

Seal the vial tightly and store in the dark, preferably at 4°C.

When recovering a stored strain, it is advisable to check the
  antibiotic markers by streaking the strain onto a selective plate.

I believe if the shipping is <24hrs you could send a stab in ice.
Hope that helps
Ben

I think the best way is to use lyophilization. The American Type Culture Collection send the strains that way.


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Can compounds be predicted from Polyketide synthases gene clusters?
I've seen a few talks on the subject. From a gene cluster, there is some decent ability to determine which domains contribute to certain functional groups in the final metabolites. It sounds like this is largely what Warp Drive Bio is trying to do. How realistic is this technology?

I would love to talk to you about this subject after my final :-) Why are you interested?

@Gergana Vandova, we were talking about whether or not Warp Drive Bio and Radiant have a realistic pipedream or not. I think that if they focus on PKS type Is, they might pull it off.

I would say that for type I polyketide synthases (PKS), this is possible. These proteins are variations on fatty acid synthases which have modules, each of which adds a two carbon unit as well as a chiral methyl group to an extending chain which may be reduced to give anything from a ketone, an alcohol to a completely reduced carbon chain.  In the illustration below you can see these 3 options, but double bonds are also possible.

Other sorts of PKS pathways (type II and III PKSs) have proteins which are harder to predict in terms of what they produce since a single protein does the extending of the polyketide chain to cyclize it, typically into an aromatic compound.  All this happens in a single protein site, so careful modelling would be required and I'd be suprised if this has been done accurately.

Note the last arrow there 'tailoring steps' - accompanying the PKS genes themselves are often a slew of acetyl and methyl transferases, additional reductases, coupling enzymes, even delivery proteins... the list goes on and on.  These steps would be hard to predict because the substrate for an o-methyl transferase isn't easily determined.
I think there are several companies trying to leverage 'best guess' bioinformatics here.  They are likely to get a good idea of the backbone, but maybe won't place every methyl and acetyl group correctly.
There are definitely people out there who think this could work to deliver diverse candidates to drug discovery.  see Radiant Genomics as well.

Each module adds a two (not three) carbon extender unit to the growing polyketide chain. Pleas correct it in your text.


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Why is beta-mercaptoethanol often added to cell culture media
Many protocols suggest that beta-mercaptoethanol is necessary for growing cells. It is a reducing agent but what does it mechanistically do for your cells. When would one not add it.

2-me is a reducing agent necessary to be added to help keep free radical oxygen from affecting mouse cells.  It is generally not necessary for human cells.
Also from S Bannai and Ishii et al., 2-mercaptoethanol improves tumor cell uptake of cystine by creating a reducing environment.

BTW, the statement about human cells is not true. The addition of bME to primary immune cell cultures, especially B and T cell cultures, is common.

Common doesn't necessarily mean necessary.

I have never used it in human B and T cell culture. I'm switching to mouse work for my post doc and trying to figure out all the differences. Thanks for this post!


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How are the various classes of E coli genes determined?
Looking at some more detailed codon usage tables, genes may be further clustered into three gene classes: Metabolic genes, highly expressed genes during exponential growth, and horizontal gene transfer. Looking at the original paper by Medique et al., they clustered the genes based on the CAI and then by a variant of k-means determined 3 classes. Note that this is different from a class II gene which is determined by the types of RNA polymerase used.
How did they end up determining what the three classes are? It seems as if they made this generalization without any proteome data. Would the same genes be classified using a protein expression data during exponential growth and stationary growth?


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How do I explain "effective number of types" to a lay audience?
I know how to calculate effective number of types. I can't figure out how to explain it to an audience that has no ecology training or background. Suppose one has 12 (for example) groups, each with a different population. Okay, so we calculate the effective number of types for that region and it's 5.7. How do I get across the concept that "out of twelve total types, with these population counts, that's the same as 5.7 types in that region"? The concept does sort of make the mind boggle a bit.

I appreciate this is a complex concept, but it would be useful if you gave a reference or two to this. I am not an ecologist and had never heard of this, but have some experience at explaining things. I checked out the top hit on a Google search, but that was clearly too complex for me. However if you suppled links to the accounts that you think are best, someone other than those in the field might be able to help.

For a lay audience, I don't think you need to explain too much of the math, just the general concept, and an example will work best.
Let's think about trees. You have 5 types of trees in a forest. If there's 200 of each, that's about as diverse as 5 types can get: we can say there are 5 species of tree in that forest. No controversy.
If, however, there's a different forest with 900 maples, 97 birch, one oak, one locust, and one willow, well, that doesn't seem nearly as diverse, does it? Sure, there are 5 tree types, but it's almost all maples with a few birch, so if you stood in that forest it might feel like there's only effectively one or two types of trees. You want to give that forest a "diversity number" that's smaller than the forest with 200 of each tree, but that somehow accounts for there still being more than just one tree type there: some number between 1 and 5.
There are of course different ways you could weight those rare versus predominant tree types (this would be q in the equation), and there's no single answer that's right for every case, but if you pick a number for how to do that (say, choose q=1), then you can get just one number that lets you say "this place has more diversity than that one" not by just counting the number of species, but also considering their proportions. It will equal the number of species if you have an even distribution, but be less than that if some are rare.
I'd give a couple concrete examples on a slide if you were presenting this to an audience (or possibly a table in a written work) with different proportions to demonstrate how it works out in practice.

(+1) I think your example with the tree species would be quite effective, and more persuasive to a general audience than considering formally-defined statistical estimates.


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Why do people feel pleasure when using roller coasters / centrifuges?
The feeling when using an amusement park unit is usually a pleasure. Why is it not a pain instead?
Are there advantages, from an evolutionary point of view, in loving this potentially dangerous activity?
Is it related to the liking for extreme sports?

I think it works the same way as horror films, we like to fear of death, but survive.

@inf3rno, Does this "fear of death, but survive" acts (brings pleasure) the whole time or only when it ends ("survival")?

Good question, I am not expert of the topic. :-) I guess the keyword is controlled fear here. So you can take pleasure in fear when you know that you what you are doing is safe. I found this article in the topic, maybe it helps. https://www.psychologytoday.com/blog/lets-connect/201002/can-fear-and-grief-be-pleasurable

Riding roller-coasters usually (unless you are psycho) induces a release of adrenaline and other chemicals, like endorphin (your bodies pre-emptive effort to combat any possible pain and stress you may be about to experience), into your body. Endorphin is a strong chemical, specifically released to make you feel relaxed and confident. Obviously this explains the natural high you may get from riding a coaster.
However, every now and then you get that person who ruins it for everyone by having a heart-attack. This person's body was not conditioned for this type of stress, and clearly they did not enjoy their ride much. Elevated blood pressure,
erratic heartbeat and palpitations...they should have instead taken a ride on the log flume. For the rest of us thrill-seekers, this type of gung-ho, take-all-comers attitude gives us a confidence boost by wiring our brains to not be overly stressed in actual emergencies.
Imagine the people out there who have grown up in small towns. You may have heard how such people can have a difficult time adjusting to the hustle and bustle of city life, especially in larger cities. This has to do with everything from their metabolism and diet, to their sleep cycle. Their body simply needs to get used to the new environment. The same goes for new combatants. Military's try their best to simulate combat for new trainees. The better the simulation, the better prepared people will be for combat. The first few combat situations for people are obviously going to be the most dangerous, being a truly foreign experience for most peoples bodies.
Physiologically it's going to push your body to the limit. After all, you sense your life is in serious danger. But as many people deal with this stress, they can start to acclimate until they ideally stay fearful, but become extremely focused on the fight. The adrenaline rush (and again, other chems) is part of what you need to get used to. If your body has a naturally stable system when exposed to these chemicals, or you have trained it to be so, then you are at an advantage compared to your peers.
https://www.psychologytoday.com/blog/threat-management/201001/adrenaline-rushes-can-they-help-us-deal-real-crisis
http://www.faqs.org/health/topics/15/Risk-taking-behaviors.html

Roller coasters release adrenaline, a chemical that is released when your body thinks it's in danger. It strengthens your body so that you could fight or flee. However, since a roller coaster is not actually dangerous, your body just feels strong and good. Your body also releases endorphins during roller coaster which makes you feel good.

Your answer makes sense, but at Bio we press people to use and mention credible sources and scientific papers


text:
Do we excrete waste in same order of food intake?
Obviously I do not expect we poop out molecule by molecule in exact order. All I am  asking is, is it possible for us to pass stool's of today's food before we poop yesterday's food. Does our GI tract act like a First-In-First-Out pipeline always?
Otherway to frame the questions is, If we consume hard to digest food 'A' first, easy to digest food 'B' next, is there a chance of B to come out before A?

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It depends on the food you have eaten. Some foods are more difficult to digest than others, and will take longer to pass through your digestive tract. Once your waste has accumulated in your colon and formed a semi-solid/solid stool, then it's likely no material can make it past that, or combine with it, but until that point, it makes sense that material from items could intermingle and get jumbled up.
The following provides rough guidelines for how long it can take to digest food:
https://www.mayoclinic.org/digestive-system/expert-answers/faq-20058340


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Duplicity Vs. Singularity of Mammals Organs
Are there known evolutionary reasons why mammals contain 2 of some organs (such as lungs and kidneys) and only 1 of some (such as liver)?

we have one brain, one heart, one pancreas, one long intestine, one short intestine, one urinary bladder, one gallbladder, one stomach...

It's just how we evolved. At some point in the past, a distant ancestor of ours had two lungs, two kidneys, one liver etc.( maybe then there was a pretty good reason for this). We evolved following that pattern and now we ourselves have two lungs, two kidneys, one liver etc.
Snakes, for example, have just one functional lung because their elongated form doesn't cope well with having two full-grown lungs. Humans on the other hand have a body shape that works very well with two lungs, so we didn't have to sacrifice one lung.
There are other examples of different organ distribution, like the octopus which has 3 hearts. Usually the more different the internal symmetry, the more distant the common ancestor.

I think liver failure is a very rare cause of death, especially among young people. So when you think about it, building and maintaining a second liver would be a huge waste of resources.