text:
Determining the appropriate bioconjugate
I'm thinking of crosslinking two proteins. The crystallographic nature of the interaction and the binding motif for each molecule is know. The paper says the intermolecular contacts (over 50; van der Waals radius 5 angstrom) are made between the motifs in these two proteins. I also know that one of the motifs on one protein has a sulfhyryl (Methionine) and for the other motif on the other molecule I (think) can use a primary amide reactive moieties. Now this is where my question is.
Would I be correct in thinking that the best cross linker to use is a heterobifunctional cross linker, with a spacer of 10 (or 5?) angstrom in order to pick this interaction up specifically and stabilise it?
I desperately need a guidance on this. I have used the life technologies crosslinker selection tool and the crosslinking technologies hand book but I can't quite figure out based on the information I have, what cross linker length I need to use. I'm not worried about the cleavability, solubility and membrane permeability parameters.
UPDATE:
I know that the binding motif on the first protein it has Tyrosine, Proline and Methionine.
Looking at the groove contacts, the second protein is interacting with this motif, using Tyrosine and Glutamine BUT the second protein also has Tryptophan, Lysine, Glutamic acid and Methionine.
UPDATE 2:
I found specially close Glutamic acid (E) and leucine (L) on my first protein, specially close to Lysine (L) on my second protein although its not in the consensus sequence for the second protein. They are less than 10 angstrom apart. is that any better? So presumably I can use the homobifunctional linker?
Many thanks in advance

Is there a cysteine available, or just methionine? Methionine won't be very useful. What about lysines?

Are site specific mutations a possibility?

Also, does the linkage need to be at the binding site? Because bioconjugate chemistry usually won't get that kind of specificity if your reactive amino acid appears elsewhere on the protein.

I can't do point mutations but I was thinking of doing linkage at the binding site since that's one of the closest contact points that is known and hence using a 10 angstrom linker would reduce non specific linkages. I'm completely new to cross linking hence any guidance would be appreciated. Currently I am planning and amide amide homobifunctional linker at 10 angstrom. Since I calculated the molecular distance from the binding residues on two proteins. I used the X-ray data and SPDBV for calculations. Is that advisable?

Your first protein is what bothers me. Tyrosine, methionine, and proline are hard to work with. On your second protein, you have a lysine, which would be useful. If there was good amine on the first protein, you could use an NHS ester homobifunctional linker. The glutamate could be modified with EDC to make it react with amines. If there are other lysines on your proteins, they will also be modified, they may not crosslink to another protein, but they will pick up your conjugation reagent.

Met does not contain a sulfhydryl, Cys does.

I have made an update. many thanks for everyones help so far :)

Could you elaborate what the aim of the study would be?

Linking the glutamate to the lysine might be possible by EDC coupling. It would react with the glutmate to make an active ester, which could react with the amine on the lysine. It might be too reactive to safely use in cells though, and would also react with water, limiting it's usefulness. But if the two proteins are already bound when you add the crosslinker, it increases the odds of a successful linkage and EDC that reacts with the incorrect residues might hydrolyze away.

@user137 That answers the question! Please consider writing this as an answer so that I can accept it :) it would be great if you could include any references to the EDC variations containing a spacer, if you think that is advisable to use for proteins that are roughly 10 angstrom apart. Also from what I read, EDC works in PBS albeit at lower efficiency right? Also would you happen to know any protocols (incubation times, conc, neutralisation, etc)? as you say the best strategy is to add it to my cells that have already made the P-P connection.

If protein 1 contains a glutamate near the binding site with protein 2 and is close enough to the lysine on protein 2, it may be possible to link the glutamate to the lysine through EDC coupling.

EDC is 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide, which reacts with carboxyl groups to form an "active ester". This ester is highly reactive with primary amines, but can also react with water or hydroxyl ions. The general reactions are outlined below:

The active ester is compound 2, which you probably want to react with the lysine on protein 2 to produce the amide in compound 3, with the isourea 4 as a byproduct. This shows that other products are possible, depending on what hits the active ester first. This reaction is most effective at pH of 4 - 5, and produces a 0 length linkage, so if you have to reach 10 angstroms across, this might not work.
EDC coupling is often followed by NHS ester formation, which is more stable than the EDC active ester, but is usually done when you intend on storing the active ester as a dry product for some time.

There are general guidelines for cross-linking protein-protein interactions, but specific parameters (i.e. cross-linker sub-types,  spacer length, linker concentration, reaction pH and temperature) are often determined experimentally. Common protein cross-linkers target reactive functional groups that are more likely found on the surface of the protein than in its "active site" or "interface" that is often buried.
Given your relatively hydrophobic, non-reactive binging motif (Tyr/Pro/Met), if you do not need a large amount of cross-linked protein sample, then you could label it with photoactivatable amino acid such as L-photo-Met. Since Met is not often found on the surface, internal cross-linking would stabilize your protein and its binding partner.
If you need a large amount of cross-linked protein (e.g. in mg) for further structural studies, labeling can be costly. You could possibly cross-link the protein (complex) crystal itself (since there were crystals as you mentioned), often just by glutaraldehyde. If the complex is there in the crystal, it would now be as solid as rock.

Glutaraldehyde would probably knock out any activity though, so the best method depends on what the proteins will be used for. I glanced through that photolabeling paper, did they say how protein yield was affected by the substitution? I've seen non-natural amino acids added through mutant tRNAs and aaRSs, but yields are typically lower.

Thank you for the response. I can't use Gluteraldehyde as I need the cells alive. Yes I have given the different parameters a though since I need the cross-linking under very specific conditions. Labelling would be costly and is not guaranteed to get integrated into my protein of interest on the cell but that is an interesting option! many thanks :)


text:
Influenza infections and drug design
Why is the neuraminidase used as a target for drugs against influenza virus instead of haemagglutinin? Is there some basic reason that this will make a more effective drug?

Can you add any research you've already done on this?

It's not that people didn't want to use hemagglutinin as a target for antivirals, it's that they haven't been able to get the antivirals through the approval process yet. There are a number of experimental inhibitors (see for example Progress of small molecular inhibitors in the development of anti-influenza virus agents) but the approval and licensing process is slow and difficult.

source: Stack Exchange

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

sort: votes


text:
Is one Short Tandem Repeat (STR) enough for a reliable identification?
The lab simulates the analysis of just one STR in the genome. Would this analysis be sufficient for a reliable identification in real life? If not, explain what could be done using DNA to identify someone more reliably.

From the phraseology this is almost certainly a homework question. The poster is presumably long gone, but the appropriate  course of action would seem to declare it off-topic.

One STR is certainly not enough for identification because the same STR could be shared by many individuals. Combinations of many STRs, however, would be sufficient for identification. The number needed would depend on how many variants of the STR exist in the population (or species, depending on what you are identifying), and what the mutation rate is (nuclear STRs mutate relatively rapidly compared to some other genetic markers, but they are still often used because they're cheap and easy to genotype).

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text:
Pearl formation process: what is it called? How does it work?
I have heard a pearl is a disease of oysters.
Astonished by the statement, I searched a bit [1] and I discovered that  it is really a protection mechanism of the oyster.
I know this defense mechanism is not unique in nature. E.g. humans can isolate foreign bodies (this happens with not-extractable bullets), as well as bees propolize foreign bodies if they can't eject them.
What is the process, the ability of those organisms, called?
How does it works? E.g. how organisms recognize foreign bodies other than other things?

[1] https://en.wikipedia.org/wiki/Pearl

https://en.wikipedia.org/wiki/Nacre#Formation


text:
Why is amylose insoluble in water?
In a handout the following is stated:

Amylose is insoluble in water, therefore a good storage compound e.g. in stroma of chloroplasts

This is with regard to the chemical structure of the molecule.
However it has left me wondering, what is it intrinsically about the structure of a molecule that makes it soluble/insoluble in water?
My thoughts at this stage are perhaps to do with whether the molecule is hydrophobic, and if that is the case - how is amylose hydrophobic?

The availibity of -OH groups for hydrogen bonding with polar water molecules is reduced in amylose due to its coiled nature (resulting in part by H-bonds between the glucose monomers).  Amylopectin is even less soluble due to the additional 1-6 glycosidic bonds on the branch chains, further reducing its H bonding potential and therefore reducing solubility in water.

Welcome to Biology.SE! Your answer sounds reasonable, however, it is likely to receive a more favorable response if you include supporting references (primary literature is best, but a textbook available online would seem sufficient for this question). ——— You may also benefit from taking the [tour] and then consulting the help pages for additional advice on [Answer] effectively on this site. Thanks!

Depending on molecular weight of amylose and because of its helical structure formed by two macromolecules makes it partly soluble in water.
Heating amylose solution leads to formation of colloidal suspension of soluble fraction and remining insoluble higher molecular weight fraction of amylose does not dissolve. On cooling this suspension, certain portion of polysaccharide precipitates. This is because of the glycosidic linkages between these glucose molecules.
Reference
Cuevas et al. Structural differences between hot-water-soluble and hot-water-insoluble fractions of starch in waxy rice. Carbohydrate Polymers 81(3):524-532

There are a couple of other questions that address this point indirectly:
here and here.
In my answers to the first of these questions I mention that amylose is semi-crystalline because of its regular extended structure. I imagine that the semi-crystalline state is more thermodynamically favourable than the solution state, but suspect that a rigorous chemical answer might be quite complex.


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Larvae appearing after many rainy days
After a few days of raining, I found these larvae in a puddle. What animal are they from?

Is the puddle still there? I would like a better picture, your location, and additional information like size and behaviour if possible. There are so many insects out there!

Thank you very much @picapica. But I already know what those things are. They are the final stage of the mosquito larvae. Named "pupa". I will post it as an answer (just in case some one else has the same doubt).

They are the final stage of a mosquito larvae, called "pupa".

btw: You are allowed to mark your own answer as "accepted" by clicking the check-mark next to the up- and down buttons.


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RE: Fasting gastric pH vs Normal gastric pH
If fasting gastric pH values are more acidic then why is it recommended to eat no more than three hours before bed time to prevent reflux. It seems at some point during sleep the stomach would become more acidic therefore make reflux worse.

Food only partially buffers the pH of stomach contents and acid is not the only esophageal irritant present in the stomach.
The goal, therefore, is to have as little as possible present in the stomach when lying down (supine) to reduce risk of gastro-esophageal reflux (GER) through the lower esophageal sphincter (LES) into the esophagus. Avoiding meals just before bed, especially fatty meals (which delay gastric emptying), may help in this regard perhaps by avoiding supine position while there is a low pH layer, formed in response to the meal, lying atop the stomach contents.
Weight loss and smoking cessation are frequently recommended to reduce GER symptoms, with some evidence to support this advice. Use of tobacco or alcohol may relax the LES and tends to be associated with GER symptoms, though trials of counseling to reduce their impact have not significantly reduced those symptoms (and another study).

It is good idea to add few scientific references to your answer.

(done - thanks for the suggestion!)


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Will a nucleic acid sequence deduced from a protein sequence be expressed from a plasmid?
I have a fasta file containing the amino acid sequence of glycogenin-1: https://www.rcsb.org/fasta/entry/6EQJ
I want to create a plasmid that produces glycogenin-1.
Is it possible to use the glycogenin-1 amino acid sequence to produce said plasmid? Or would one need the nucleic acid sequence to do so?

Companies like Origene sell pre-made plasmids in a variety of backbones, with or without epitope tags, for a relatively small amount of money. For example, human glycogenin-1 for US$420.

Thanks @MattDMo.  However I don’t need to purchase a plasmid, I need to make one.  If I had the nucleic acid sequence I would just use that, but all I have is the amino acid sequence, so I need to know if I can use the amino acid sequence to make the plasmid.

You just need to reverse-translate the protein sequence (e.g. on the free online IDT codon optimization tool) and include it in a common plasmid backbone. Basically in order to answer we need to know exactly what you are trying to build.

What happened to the answer to this question and the comments on that answer?  Someone decided to just delete it?

@user1454024 The answer was deleted by the author. Users with high enough reputation (like me) can still see it and the comments, though, and I have two responses. First, you don't need to optimize the codons like you suggested, because once the transcription machinery is in place on the open reading frame, it skips ahead 3 bases (1 codon) at a time. So, unless you expressly design the plasmid to have two overlapping ORFs, you don't need to worry about that. Second, the nucleic acid sequence of your protein is available online, so you don't have to reverse-engineer your protein sequence. [...]

[...] The sequence is accession number NM_001184720.

The NM sequence is for the wild-type protein, not the Tyr->Phe mutant that you have, if that makes any difference.

I lack the knowledge to fully answer your question but I can give some potentially useful pieces of information:

In theory you can easily in-silico reverse translate a peptide
sequence to an unambiguous nucleotide sequence using the GMOs
optimized codon usage. I can share a Python script for that.

Also you could easily search for the 'real' nucleotide sequence in
databases. For example use 'Blast' to find the gene of your peptide
sequence.

But attention! There are known cases of codon-optimized sequences
causing bad protein folding or even (paradoxically) worse expression
levels than the native sequence.

There is software that helps with the design of plasmids, also in
light of use of unique restriction sights, helping to decide which of
your restriction enzymes are applicable.


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Estimates of historical human population size
What are the estimates of minimum historical human population size, and how are they obtained from the current human genetic diversity?
I seem to recall a Scientific American article from over 30 years ago claiming a figure of 500-1000, but I can’t find any estimate now.

What exactly is your question?

I have modified your question slightly to make it more acceptable. If it is not what you meant do change it. It would be helpful to know precisely what you mean by "historical" — is it the pre-emergence from Africa I have assumed in my answer? Also, as a new user, please finish reading the [tour] which has information about using this site.

Although I cannot find the Scientific American article to which the poster refers, I assume that the “historic human population size” is the size of the human population in Africa before it underwent the expansion that accompanied the emergence from the African continent. Some important papers on this subject were published in the late 1990s (somewhat later than 30 years ago) and there is a suggestion in one of earlier estimates that I have not yet found a reference for.

There is an implication in the Harpending et al. paper (below) of earlier estimates of the order of 1,000. I will try to find the source (help on this welcomed).

Harpending et al. published a paper in PNAS of February 1998 in which they conclude an effective population size of the order of 10,000 individuals for most of the Pleistocene.

Reich and Goldstein published a paper in PNAS of July 1998 in which they conclude a maximum pre-expansion population size of 5,900.

A more recent study by Huff et al. published in PNAS in February 2010in which they estimated that the effective population size of human ancestors living before 1.2 million years ago was 18,500, and in which they rejected all models where the ancient effective population size was larger than 26,000

Why should the later estimate be more likely than the earlier ones?
Although the details of the calculations are complex (or at least too complex for me), it appears that the genetic markers that are used are crucial, and that it is important to have markers that represent rare mutational events. The earliest studies apparently used mitochondrial genes and the non-combining parts of the Y chromosome as markers. (These are used and are valid for studies of more recent time.) The limitations in these resulted in a shift to Alu repeats and microsatellites in the two 1998 papers, respectively. The 2010 paper used the insertion of the longer LINE repeats, which occur about one tenth as often as Alu insertions.
There is a Wikipedia article on this topic that may be also be of interest.


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Why doesn’t dust interfere with the adhesion of geckos’ feet?
Setup:
The way a gecko's feet function has been a captivating but now relatively well understood phenomenon. They have many small spatula on the feet that exploit electromagnetic van-der-Waals forces on the walls to which they stick.
This concept has been developed in "nano-tape" a product which is adhesive the same way a gecko's feet are. And there has been no shortage of folks trying to create "spiderman gloves" to re-create this, one interesting example being this attempt by Elijah Animates to scale a flat rock climbing wall.
Elijah found that the nano-tape gloves were rendered ineffective by chalk dust on the wall which would coat the micro-structures and prevent them from sticking.
This leaves me very confused. I have often seen geckos when I travel to India in some extremely dusty conditions. For example, far MORE dusty than a well chalked climbing wall. Despite that, these geckos STILL stick perfectly well to all manner of surfaces, even glass walls.
Question:
What are gecko's feet doing that is fundamentally different than the nano-tape which allows them to operate in extremely dusty environments successfully? It clearly goes one step beyond merely exploiting the Van Der Waals forces but also somehow "removing any debris that is stuck".
This I also find hard to explain because I don't think I have ever seen a gecko "shake its legs off" similar to how a dog shakes water off. The mechanism of debris removal is probably subtler than that.

This is a very interesting question. Basically (and this is the short answer), geckos possess a unique self-cleaning mechanism in their feet which synthetic nano tapes do not have. This capability allows geckos to maintain their adhesive properties even in dusty environments.
Gecko Feet Mechanism
Gecko feet are covered with millions of microscopic hair-like structures called setae, which branch into thousands of even smaller spatulae. These structures allow geckos to adhere to surfaces through Van der Waals forces, which are weak intermolecular forces that become significant at the nanoscale. When a gecko walks, the lateral movement of its feet creates friction that dislodges larger dirt particles, while smaller particles fall into the folds of their skin, effectively cleaning the setae as they move. The self-cleaning ability of gecko feet is attributed to the hierarchical structure of the setae and spatulae, which allows them to dislodge contaminants efficiently. Experimental studies show that geckos can regain about 80% of their adhesive strength after just a few steps on contaminated surfaces, thanks to this mechanism (see references 1, 2 and 3 for more details).
Synthetic Nano-Tape Comparison
In contrast, synthetic nano-tapes inspired by gecko feet often lack the same level of self-cleaning efficiency. While they can mimic the adhesive properties of gecko feet, they typically do not perform well in dusty conditions. The synthetic versions may rely on larger microhairs that do not effectively roll off dirt particles, leading to a significant loss of adhesive strength after contact with contaminants. Moreover, many synthetic adhesives use glue, which can degrade over time and lose adhesion, unlike gecko feet that remain sticky without any additional substances. Although some synthetic tapes have been developed to replicate the self-cleaning effect, they have not yet matched the natural efficiency of gecko feet in real-world conditions.
Conclusion
In summary, the fundamental difference lies in the gecko's natural ability to maintain adhesion through a sophisticated self-cleaning mechanism facilitated by its unique micro- and nano-structured feet, whereas synthetic nano-tapes often struggle with dirt retention and adhesive longevity due to their reliance on larger structures and glue-based adhesion methods (see references 4 and 5 for more details).
References:

Robust self-cleaning and micromanipulation capabilities of gecko
spatulae and their bio-mimics
Gecko adhesion: evolutionary nanotechnology
Dynamic self-cleaning in gecko setae via digital hyperextension
Robust self-cleaning and micromanipulation capabilities of gecko
spatulae and their bio-mimics
Carbon nanotube-based synthetic gecko tapes

I don’t usually read or vote on organismal biology questions or answers because their quality is generally low, but this is an example of a first-rate answer to a perceptive question. We could do with more.

Thanks for the great answer.


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Understanding the use of English tenses in biological journal articles
My colleague and I (second language speakers) got in an argument in understanding the sentence:  " however, how this complexity and diversification have been achieved remains rather poorly understood.” in the context of the below Abstract’s report.
In short, the question is:
Does this sentence valid till the end of this report? i.e. the complexity problem continued and not solved in this study?
His understanding that this sentence stated in this report as a past context or past story, i.e. the abstract is telling us how our knowledge was? and this study solved and answered how this complexity happens and achieved.
Reference:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852327/
I know these questions are mostly about understanding English rather than biology!
I appreciate your help.

I’m voting to have this question transferred to English Language and Usage under the tab "technical" if others regard it as off topic here.

I regard this is more of a question for SE English Language and Usage under the tag “technical”, and will vote to move it there. However, as the answer relates to reading papers in molecular biology, I provide an answer here.
Linguistic interpretation without context
The tense used in the phrase “X remains poorly understood”, taken in isolation, suggests that this is the situation now. Hence, it is the situation at the end of the study.
However…
Interpretation in context
This is the Introduction section of the paper. In the Introduction to papers reporting experimental biological research, it is usual (and helpful to the reader) to explain the background to the study and why it was undertaken. In this case to explain that the incomplete understanding of the subject justified further studies such as the one to be described.
This is made clear at the end  of the Introduction, where one often indicates in a sentence what the work to be described adds to knowledge: “Our results show that flagellum originated very early, before the diversification of contemporary bacterial phyla…”.
So the minimal implication is that as a result of the work described “X is now better understood”. And that is clearly the case here.
This is borne out by the final paragraph of the Results section in which the authors emphasize the contribution to knowledge that their work has made. You don’t get published in PNAS by saying that you have left the field still in the dark!
Why not use a different tense and say that you the problem has been solved?
An alternative would have been to write:
“Before this work was undertaken X was poorly understood”
The reason for not doing this could either be “scientific modesty” (also known as don’t antagonize the referees by appearing arrogant) or acknowledgement that, despite the significance of the work presented, there are still aspects of the problem that are not understood.

Your Answer is awesome! Thank you very much

@A.Qatar I am glad that you found it useful. The form on SE is to "accept" an answer if you think it correct and has answered your question. This informs others that the poster thinks the question has been dealt with (so they can prioritize other questions) and rewards the person who answers. However, I think it is best to wait several days before accepting an answer, especially if you cannot be certain it is correct. A better answer may appear, or others may criticize the answer that seems at first ok, either by comments or down votes. So take your time.


text:
What Ultimately Controls DNA Transcription?
Transcription of DNA and further splicing of mRNA is regulated by various transcription factors, small nuclear RNAs and so on; similarly such related mechanisms as transposition of transposons.
All such factors and mechanisms, including those linked to inter-cellular signalling mediated by peptides and various so-called epigenetic enzymatic processes, require and are dependent upon transcription itself, in the first place of DNA codons.
What mechanism then is supposed ultimately to control the expression, eventually as peptides translated from mRNA, of information encoded in DNA; if it is not peptides thus encoded? That is, since transcription depends on transcription factors which themselves require transcription requiring further transcription factors, does this mean that in the entirety of its function, DNA controls itself?
How then can DNA and its transcription be conceived as a such a self-controlling function?

Transcription of DNA is ultimately controlled by "various transcription factors, small nuclear RNAs and so on" in the cell.
The molecules which make up the "various transcription factors", etc. are already present in the cell when a new transcription begins.  As you note, most all of these molecules are themselves dependent on the transcription of DNA, but also of the availability of component molecules (e.g. nucleotides, amino acids) and of processing mechanisms such as ribosomes.
So, a new instance of transcription requires a working cellular environment, and that environment was created and maintained as directed by DNA molecules at an earlier time.  Usually those DNA molecules were exactly the same as the ones from which the transcription is proceeding. Occasionally, those DNA molecules would have been physically different, but adequately compatible, such as the source chromosomes which were copied during mitosis to create the current DNA molecule.


text:
What species is this orange mushroom in Romania?

So I've found these mushrooms near a ditch on a field a few days ago in Romania. Can anyone help me with identifying what species of mushroom is this? The size of a mushroom is about 3-6 cm in diameter. Thanks and a happy new year.

Hi griffinwish. Please update your question with the approximate size of your specimen, and please provide any additional information or pictures that are possible. Images of both the tops and undrsides of mushrooms are preferred for accurate ID. See [tag:species-identification] tag question guidelines here. Doing so will increase the positive voting response your question receives as well as increase the odds of receiving a good/accurate answer. Thanks!

This is most likely Kuehneromyces mutabilis or sheated woodtuft. It is quite common in Romania where it is named Gheba ciobanilor.
Quote from Wikipedia about the diagnosis:

The clustered shiny convex caps are 6–8 cm in diameter. They are very hygrophanous; in a damp state they are shiny and greasy with a deep orange-brown colour towards the rim; often there is a disc of lighter (less sodden) flesh in the middle. In a dry state they are cinnamon-coloured.
  The gills are initially light and later cinnamon brown, and are sometimes somewhat decurrent (running down the stem).
  The stipe is 8–10 cm long by about 0.5–1 cm in diameter with a ring which separates the bare, smooth light cinnamon upper part from the darker brown shaggily scaly lower part. This type of stem is sometimes described as "booted".
  This species always grows on wood, generally on stumps of broad-leaved trees (especially beech, birch and alder), and rarely on conifers.
  It is found from April to late October, and also in the remaining winter months where conditions are mild. It is often seen at times when there are few other fungi in evidence.

Further details can be found here in English
or here in Romanian


text:
Can a virus infect a virus?
As far as I know a virus can infect any cellular organism from a bacteria onwards, including protists, algae, plants, and so forth.
But can a virus infect a virus?

No, it cannot. Viruses infect cells, in order to use the cellular machinery to replicate themselves - viruses themselves do not possess such a machinery, so speaking of one virus infecting another is meaningless.
This does not mean that viruses do not interact: when two viruses co-infect the same cell, the progeny virions may contain parts of the genomes of both viruses. This is how genetic recombination occurs in HIV.
An even more famous example is gene reshuffling of influenza viruses, where an animal virus exchanges its genes with a human virus, producing a new human strain. In the popular culture some of these a famously named after animals whose virus contributed or animals where the reshuffling has occured (bird's flu, swine flu, etc.)
Update
It is worth mentioning the satellite viruses, which are viruses that lack the proteins necessary to catalize the replication and possibly even the genes coding for their capsid proteins (in which case they are more properly called satellite nucleic acids rather than satellite viruses). These viruses are dependent on a helper virus to carry the missing genes. This is not characterized as parasitism, but it is rather close.
Update 2
A special type of satellite viruses, called virophages, actually do exhibit characteristics of parasitism in respect to the helper virus:
Unlike satellite viruses, virophages have a parasitic
effect on their co-infecting virus. Virophages have been
observed to render a giant virus inactive and thereby
improve the condition of the host organism.


text:
Are pheromones capable of activating changes to the Phenotype of a complex organism?
I know that pheromones are means of communication between the same species, but are they capable of changing the phenotype of an organism, may be influencing the expression of the genes of a said organism.

Pheromones are means of communication between individual within a species, not between species.

[A]re [pheromones] capable of changing the phenotype of an organism[?]

Yes! It actually necessarily does, by definition. If a chemical produced by an individual does not affect the phenotype any individual of the same species, then it is not a pheromone! You will note that behaviour is part of an organism phenotype.
Pheromones can have drastic impact on an organism phenotype. Most notable examples are from social insects, such as caste differentiation in termites (Matsuura et al. 2010).

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text:
What allows the hypothalamus to detect a lack of thyroid hormones?
On the website www.yourhormones.com it is written:

"If there is insufficient thyroid hormone available for the brain, this will be detected by the hypothalamus and thyrotropin-releasing hormone will be released into the blood supplying the pituitary gland."

What allows the hypothalamus to detect a lack of thyroid hormones? Are there chemoreceptors in the bloodstream that send afferent signals to hypothalamus when the concentration of thyroid hormones is low (similarly to how chemoreceptors inform the cardiovascular center of the medulla oblongata in the brain stem when there is a lack of oxygen and/or excess of carbon dioxide)?

The thyroid hormone, thyroxin has a multitude of effects in various cells of the body. It is a lipophilic hormone and acts via nuclear receptors, i.e. the receptors for the hormone are not on the cell surface but inside it. This hormone-receptor complex then travels into the nucleus to attend to transcriptional changes.

The picture above is for steroid hormones but is almost similar for thyroxin too.
Inside the cell, the effect of the hormone depends on which cell it is in. For thyroxin - in heart muscles, it increases cardiac contractility, in fat cells, increases fat catabolism, and in the very same way, in the hypothalamus, its function is to reduce the production of TRH. And the control of this production is at the level of gene transcription.
Hence there is a lovely feedback loop that is formed. Increased thyroxin would lead to reduced TRH production and vice versa. So the hypothalamus responds to the thyroxin hormone by regulating the production of TRH. There is nothing special that the thyroxin is doing here. It just has different effects in different cells and in this particular cell (the neurons of the hypothalamus), the effect happens to be its own feedback loop regulation (via TRH).
The effect of thyroxin is through its receptor that is an intracellular protein and is more or less the same in all cells.
Chemoreceptors are a different ballgame. They sense changes in pH, pO2, and other biochemical parameters through their direct effect on neurons and their firing. Although their functioning is not particularly clear, they interfere with channel conductivities in particular neurons. There is no receptor and transcriptional changes as in thyroxin.

By saying that chemoreceptors "interfere with channel conductivities", do you mean that they, for instance, increase the conductivity of afferent neuron axons that signal the cardiovascular center to modulate breathing when oxonium ion or CO2 concentration is high?

Yes something of that sort. A direct biophysical change perhaps... If that's the right term.. I don't know


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Relationship between fatty acid chain and saponification number
Why do long chain fatty acids have low saponification number? What is the relation of fatty acid chain( R)  with saponification number?

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


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Why do birches have a white bark?
Several species of the tree genres Betula have a white bark,especially when they are young. This is quite peculiar to trees - at least in central Europe; so I'm wondering if there is a ecological reason behind it.
The first idea I have is that they protection against the sun. But normally protection of nature against the sun is to make the opposite: put more pigments in the skin, so that the sun does not damage the underlying DNA.
If this is the explanation, how do other tree species protect against this?

They produce a rare pigment of white color, called betulin. Found the article about it: https://tmtml.blogspot.com/2017/12/why-birches-are-white.html

It is protection against rapid warming of the cambium layer. A lot of far northern timber has light colored bark which reflects sunlight. The rapid heating from very cold after sunrise can actually damage or even split the bark of dark colored species. This is called sunscalding.

Note that aspens, which grow at high elevations in the mountains, also have very light-colored bark.  But oddly enough, the conifers growing in dryer areas at the same elevations generally have dark brown to greyish bark.

conifers of course provide their own year long shade.

Not usually around sunrise, unless located in a dense stand.

@jamesqf thick, rough or rugose bark also aids in resisting it, conifers also experience less dramatic dormancy which helps resist the effects. Different solutions to the same problem.

The definitive study seems to be Karels, TJ & Boonstra, R "Reducing solar heat gain during winter: The role of white bark in northern deciduous trees" Artic vol 53 no 2 pg 168 (2003).

There is also a lot of other circumstantial evidence supporting this theory. The birch species that exhibit white bark, in N. America, B. papyriferia, B. populifolia, and B. cordifolia, are all pioneer species inhabiting barren, open habitats and thus exposed to more light. The more shade-tolerant, forest-dwelling birches, B. alleghaniensis and B. lenta, have darker bark, probably because their habitat has more tree trunks to absorb or block out the light so they didn't face the same selection pressure. Also what @jamesqf said about Aspens fits this pattern: they are also pioneer species.


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What determines if a compound is primarily taken up by the lymphatic extensions rather than the portal vein blood supply in the intestinal villi?
I am currently studying the intestinal absorption/transport systems, but am confused about one part specifically. There are hydrophilic and lipophilic compounds (to varying degrees), and they get absorbed by different methods.
As far as I can tell there are 3 main ways of absorption in the intestinal wall:

Passive diffusion of lipophilic compounds through the membrane.
Passive diffusion of hydrophilic compounds through pores and gap junctures.
Active transport of larger molecules by transport proteins.

But once a compound passes the enterocyte absorption cells in the lining of the villi of the intestine, there are primarily two paths into systemic circulation:

Capillaries of the blood supply from the hepatic portal vein, leading to the liver and first pass metabolism.
Lymphatic uptake through the extension of the intestinal lymph system in there.

From what I can tell anatomically, both of these are somewhat intertwined/overlapped to an extend — but which properties of a compound determine whether it is primarily taken up by the lymph system (getting it to the blood supply eventually circumventing first pass hepatic metabolism) or wether more of it is taken up by the local portal vein capillaries? Is it small differences outside of the general hydro/lipophilic nature like size etc.?
Please correct me if I'm misunderstanding some of these basic anatomic concepts. I would appreciate if someone can tell me whether there is a set of parameters involved in this biochemical branching.
I just read the lacteals, the lymphatic vessels in the villi, absorb digested fats. Does that mean the more lipophilic a compound is the more likely it is to be absorbed by the lymph over the portal vein capillaries? That sounds a bit too simple for me. There must be more factors involved.

The path used for a particular compound is determined by several factors:
Affinity for Plasma Proteins: Compounds with a high affinity for plasma proteins are more likely to remain in the bloodstream rather than diffusing into the lymphatic system.
Lipophilicity: Highly lipophilic compounds are more likely to be absorbed into the lymphatic system because they can be incorporated into chylomicrons, which are too large to pass through the capillaries of the blood supply and thus enter the lacteals.
Molecular Size: Larger molecules, especially those larger than the fenestrations in the capillary endothelium, are more likely to enter the lymphatic system for the same reason as above.
Solubility: Compounds that are not water-soluble may need to be transported in association with bile acids or incorporated into micelles to be absorbed. After absorption they are often repackaged into chylomicrons and enter the lymphatic system.
Transport Mechanisms: Some compounds require active transport mechanisms to cross the intestinal epithelium. These mechanisms can be selective and influence whether a substance enters the blood or the lymphatic system after absorption.
Chemical Stability and Metabolism: Some compounds may be metabolically unstable in the gastrointestinal tract or the liver. If they are metabolised in the enterocytes, the metabolites may have different properties that affect their route of absorption.
Charge/Ionisation State: The ionisation state can affect the compound's ability to cross the lipid-rich cell membranes. Non-ionized (lipophilic) forms are more likely to be absorbed through the lymphatic system, while ionized forms are generally more hydrophilic and absorbed into the portal circulation.
Formulation: The pharmaceutical formulation of a compound can influence its absorption. For example, lipid-based formulations may enhance lymphatic uptake of certain drugs.
Note that these paths are not mutually exclusive. The relative contribution of each factor varies with the specific properties of the compound in question. The extent to which each path is used can vary greatly and is influenced by these factors, and of course this implies that a molecule may use both paths, and this is determined by metabolites utilising different pathways, partial absorption by both routes, regional absorption variations and variable physiological conditions


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What is the phenomenon when animals mimic other animals in order to survive?
The caterpillar Hemeroplanes triptolemus adopts the appearance of a snake when it detects danger. What is this phenomenon called in which animals mimic other animals in order to survive? Is it morphological adaptation, if not why not?

Deimatic display:

Deimatic behaviour or startle display means any pattern of bluffing
behaviour in an animal that lacks strong defences, such as suddenly
displaying conspicuous eyespots, to scare off or momentarily distract
a predator, thus giving the prey animal an opportunity to escape.

This could also be referred to in more general terms as Batesian mimicry.

In Batesian mimicry the mimic shares signals similar to the model, but
does not have the attribute that makes it unprofitable to predators
(e.g., unpalatability). In other words, a Batesian mimic is a sheep in
wolf's clothing. It is named after Henry Walter Bates, an English
naturalist whose work on butterflies in the Amazon rainforest
(described in The Naturalist on the River Amazons) was pioneering in
this field of study.

This is distinct from aposematism, in which a positive defence mechanism is present and advertised:

Aposematism is the advertising by an animal to potential predators
that it is not worth attacking or eating. This unprofitability may
consist of any defences which make the prey difficult to kill and eat,
such as toxicity, venom, foul taste or smell, sharp spines, or
aggressive nature. These advertising signals may take the form of
conspicuous coloration, sounds, odours, or other perceivable
characteristics.

The phenomenon whereby one animal mimics another is called mimicry by zoologists as opposed to camouflage, although plants can be mimcs as well.
There are this many varieties of mimicry, so it's best to refer to the wiki reference:
2.1 Defensive
    Batesian
    Müllerian
    Emsleyan/Mertensian
    Wasmannian
    Vavilovian
    Gilbertian
    Browerian
2.2 Aggressive
    Predators
    Parasites
2.3 Reproductive
    Bakerian and Dodsonian
    Pseudocopulation
    Inter-sexual mimicry
2.4 Automimicry

https://en.wikipedia.org/wiki/Mimicry
Is it a morphological adaptation? It effects pigmentaiton and morphology and it is encouraged by random mutations which confer to the mimic a resemblance which has an evolutionary advantage, i.e. a resemblance to an animal which is avoided by predators.


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Is there an established algorithm to produce a hash number from a person’s DNA?
It is often said that a person’s DNA uniquely identifies that person. Is there an established algorithm that can/could take values of a specific DNA sample to produce a digit string unique to its source, perhaps as a hash of the quantification of DNA components?
I am a software engineer with very little knowledge of genetics, so I’ll stipulate this may be a dumb question for those skilled in the art.
However, as hash spaces are easily defined that can uniquely represent trillions of elements, it seems me that this should be possible and likely has been worked out.

This rather assumes 100% copy fidelity in every cell of the body as a basis, that's not quite the case.

One slight correction. Not all humans have different DNA sequences — identical twins start out the same in this respect.

As a link to a paper is not an answer, and I cam not competent to summarize the paper, I just provide this info in a comment. Have you seen Zobrist's "Ordered Minimal Perfect Hash of the Human Genome and Implications for Duplicate Finding"? It requires membership of IEEE or institutional access.

There are various approaches based on sequence k-mers that do more or less this. I don't off the top of my head know which ones are the most trusted for minimizing collisions, which appears to be your motivation. For a general purpose k-mer library you might look at khmer. For something a little less biology focused you might look at murmurhash, which I believe is nonetheless used extensively in bio applications.
MinHash has been used fairly extensively to generate sequence hashes efficiently in large nucleotide sequence collections. However, it relies upon a summary that may not guarantee uniqueness at the level you are interested in.
For a thread discussing different approaches and with more background, see here.
If you are interested in human sequences specifically, there is a good amount of material out there on constructing unique hashes, though I'm not personally so familiar with it. Here is one reference at google-random, here is another.
It's also true as stated in the comments that the sequence of an individual is noisy. I would argue that there is a strong enough central tendency in the distribution of sequences for a human that it's still a worthwhile exercise, but understanding this shortcoming will be crucial for interpreting data (especially given the error-prone nature of sequence reconstruction via sequencing and assembly).


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Is the pyruvate dehydrogenase reaction considered part of the Krebs Tricarboxylic Acid Cycle?
I’ve encountered questions where I’m asked to find out the CO2 released, the number of oxidative carboxylations etc. in the Krebs tricarboxylic acid cycle. I always include the pyruvate dehydrogenase reaction (sometimes termed the ‘link reaction’) that converts pyruvate (from glucose) to acetyl-CoA which then feeds into the Krebs cycle. However my answers are only considered correct for certain questions, while for the others they are not.
How do I decide if a reference to the Krebs cycle includes the pyruvate dehydrogenase reaction?

It would help to get examples of such specific questions, where you got it right or wrong, to understand the point of confusion.

I have rewritten your question in a format that is more precise scientifically and focusses more on the scientific question, rather than your person difficulties interpreting your teachers' questions. If after reading and understanding my answer you still are puzzled by your marks you should ask your teachers why you were marked incorrect in particular cases. I see from an internet search that the term "link reaction" is used at an elementary level. This is imprecise and not used by biochemists, which is why I have substituted pyruvate dehydrogenase reaction.

It is outside both the remit and competence of this site to divine the intentions of university teachers in questions that they set to students. What we can do is explain the scientific points that may be at issue, in this case why:

the Krebs tricarboxylic acid cycle does not include the pyruvate
dehydrogenase reaction.

First is the obvious fact that the pyruvate dehydrogenase (PDH)
reaction is not part of this cycle of linked reactions, any more than
the conversion of glutamate to α-ketoglutarate (2-oxoglutarate) is.
But even if you consider acetyl-CoA as somehow “starting” the cycle,
the PDH reaction is not required to generate it. Acetyl-CoA can also
be produced from the breakdown of fatty acids or certain amino acids.
Further, acetyl-CoA produced from pyruvate need not feed into the TCA
cycle: in some circumstances it is converted to malonyl-CoA and to fatty acids.

The diagram below (a fossil of my biochemistry lecturing career) illustrates some of the various possible inputs into the TCA cycle in a general sense:


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Does reversion of resistant strains to wild-type only occur when no more drug pressure is exerted
We always read that wild-type reversion of a resistant strain occurs when no more drug pressure is exerted. Could resistance reversion also occur under drug pressure, but from a drug other  than the one to which the virus is resistant.
To illustrate my question, let’s assume an HIV strain resistant to a specific anti-retroviral drug class (e.g. NNRTI drugs). Would NNRTI-resistance reversion to wild-type HIV occur under the pressure of another drug regimen (e.g. PI drugs) or does resistance reversion only occur when no more drug pressure at all is exerted?

Welcome to SE Biology. Your question is good, but could be improved with a reference to support your initial assertion. Your "reputation" indicates you have not yet completed the Tour. We recommend new users do so, and perhaps view the Help on asking questions. And it is a good idea to check your title carefully. One with a spelling mistake and a word missing does not create the best impression. (I've fixed it).

I am not an expert on HIV but I am answering based on general principles.
This is a typical example of selection of individuals/populations with different fitness.
Reversion to wild-type (WT) would happen if the WT has higher fitness in that environment. Assuming that WT is the fittest under drug-free conditions, it is not difficult to understand that the WT population will outgrow other mutants.
For your question — "would a drug resistant HIV population revert to WT under treatment with other drugs", the simple answer would be no.

Explanation
HIV generally acquires resistance against different drugs quickly because it has a high mutation rate. In your example case, the HIV population that is resistant to the new drug will outgrow other populations if we assume that the selection is strong. There would not be any reversal to WT because WT would also be unfit in the new environment. If the selection is weak then the population genetic diversity would depend on the relative fitness of different genotypes.
There may also be pleiotropic effects: mutations that provide resistance against one drug can also possibly provide resistance against other drugs. This is well known in case of bacteria and there are many reports for HIV too (Rhee et al, 2010, Other Google Scholar Hits).


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Where do Red Blood Cells use energy?
I know that RBCs use glycolysis of glucose to lactate to produce most of their energy, but, if they are just carrier cells, where do they use the energy?

Erythrocytes are far more than inert "bags" of oxygen. They are complex, highly specialized cells and, like all cells, they require a number of basic processes to be maintained to work properly.
A good example (out of many) of why red blood cells need energy would be the active transport of ions across the membrane, a mechanism important for any type of human cell.
Quoting an article by Knight & Welt (J General Physio, 1974):

The human red blood cell maintains a high intracellular potassium (K) and low sodium (Na) apparently by balancing passive movements of the ions with their active transport in the opposite direction. Thus the cell extrudes Na and accumulates K in a linked process (...). The component of Na-K transport (...) is dependent on adenosine triphosphate (ATP) in the cell.

A visual explanation of how export of sodium and import of potassium are linked to the consumption of ATP:

This means that to maintain correct gradients across the membrane (important to maintain osmotic level, and to provide a potential energy exploited in other import-export processes) the cell must continuously spend molecular energy.
Producing ATP in red blood cell is also important to maintain a pool of phosphate-donors for phosphorylation signals, involved in cell signaling for example.
Interestingly, it was also shown that releasing ATP is also a way for erythrocytes to communicate with their environment, possibly to stimulate microvessel dilatation and thereby allowing proper circulation of oxygen near the destination site (see Ellsworth et al, Acta Physiol 2016 for a detailed review).
All these processes require ATP, and therefore a continuous metabolic activity.


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Chorophyll and photosynthesis in plants with coloured leaves
Do plants that have only coloured leaves (e.g. ‘ornamental’ plants) contain chlorophyll and perform photosynthesis?
If they don’t, how do they obtain energy and metabolic intermediates?

Most of ornamental (often variegated ) plants do performs photosynthesis. They do have chlorophyll even if their color is not green. They have non-green color due to various different pigments. These extra color has their own functions like blocking harsh sunlight or protection from insects (Karageorgou and Manetas 2006).
In many non-green plants carotenoid content is way higher than chlorophyll. One of the main functions of these carotenoids is to expand the range of wavelength where photosynthesis can happen (Hashimoto et al 2016). This is especially important for such plants living in low light conditions or other stress factors are dominant.
Some comparison of content in different color leafs of Acer saccharum is enlisted in table below. Image is taken from (Junker and Ensminger 2016)

Photosynthetic activity of such plants can be measured by chlorophyll fluorescence techniques (Borek et al 2016). Photosynthesis performance of many of these plants (like Actinidia kolomikta) is actually properly maintained (Wang et al 2016) and does not have high Photosynthetic Cost.
Just to extend this answer for little general information, plants without any chlorophyll (like Cuscuta europaea) are often parasitic plants and they need host to survive and get nutrients.

Your answer should stick to the point in the question and answer that. The illustration of a plant you cite has green leaves. You do not say whether plants with e.g. red leaves contain chlorophyll. That was the question. You should do this and cite evidence for your statement.

@David , it was implied in my first sentence. However, now I have explicitly mentioned it.

Fine. But it needed spelling out.


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What is the name of this moth and why does it have an extra wing?

Moth of length 15mm. Seen in Kerala, India on March 2019. Third Unusual wing part visible. Without mobile flash the colour of moth visible is completely black.

This isn't a moth, it's a planthopper (Order Hemiptera, suborder Auchenorrhyncha, infraorder Fulgoromorpha, Superfamily Fulgoroidea [in which there are over twenty families worldwide; which is represented here I cannot guess]).  The "extra wing" is the right hind wing displaced (more than likely due to injury).

@ArthurJFrost Can you please make this comment into a full answer? Then you can get the credit for it. Additionally, answering in the comments in not liked here.


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Can a symptomatic, recent recipient of live attenuated dengue vaccine Qdenga transfer the virus to mosquitoes if bitten?
Can a symptomatic, recent recipient of live attenuated dengue vaccine QDENGA transfer the virus to mosquitoes if bitten?

When you say "the virus" do you mean the original Dengue virus? Or do you mean the attenuated yellow fever virus with a couple Dengue genes?

Dengvaxia is the older yellow fever-based vaccine, Qdenga is based on attenuated DENV2.

@timeskull Ah, thanks for that clarification!

The possibility of mosquitoes becoming infected with vaccine-strain DENV by taking a blood meal from a vaccinated human has been found to be low. Transmission of vaccine-strain DENV to unvaccinated people was found to be "very unlikely", but not ruled out completely.
From Limited Transmission Potential of Takeda’s Tetravalent Dengue Vaccine Candidate by Aedes albopictus:

It is critical that live-attenuated dengue vaccine viruses will not be transmitted by mosquitoes from vaccinees to the unvaccinated population, and part of the vaccine safety evaluation requires confirmation of low mosquito transmission potential.[13–18] To be transmissible by mosquitoes, the virus needs to be able to infect the mosquito midgut (infection), escape the midgut infection barrier, replicate in the salivary glands (dissemination), and be released into the mosquito saliva (transmission).[19] The TDV viruses were previously found to be inefficient at infection, dissemination, and transmission in Aedes aegypti, the primary vector of DENV.

TDV (Tetravalent Dengue Vaccine) refers to QDENGA in the above quote.
QDENGA is attenuated by serial passage through dog kidney cells, so the virus becomes better at infecting and replicating in those cells but worse in human and mosquito cells. The vaccine strains (there are 4 separate vaccine-strain viruses, one for each natural serotype of dengue) are much less effective than wild type at infecting mosquitoes, even for blood with the same concentration of virus particles. Vaccine-strain DENV on average reaches 1000x lower concentrations than wild type, these two effects are cumulative. This study couldn't measure the likelihood of transmission because 0 vaccine-treated mosquitoes (out of 186) developed measurable levels of virus in the salivary glands, which are what can transmit the virus to human hosts.

I wonder if the levels of virus in mosquitos' salivary glands are sufficient to infect dogs, now that the new strain is more infectious for dogs, and apparently they can be infected.

well, the new strain was passaged through dog cells, but that doesn't guarantee it's particularly good at infecting dogs. To give a crude analogy, if you forced humans to adapt to living in water for 6 generations, they still wouldn't be able to compete with fish.


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Function and expression of pseudogenes
Can pseudogenes be transcribed into mRNA and translated into functional proteins, or should they be regarded as functionless mutated genes?

By definition, a pseudogene has lost its ability to be transcribed or generate functional protein. If you reinstate that ability, it will no longer be a pseudogene.

Attention: Wikipedia is wrong about its definition of pseudogenes. Please see my answer below for a) one of many example of the official organization that defines "pseudo-gene" gene-type for individual genes (NCBI), which lists functions for specific individual pseudogenes b) One of many research articles studying transcribed pseudogenes (here: those which are even translated). wikipedia cites outdated paper from 80ies

A subset of pseudogenes can have a function - even if not translated: For one possibility see the official record for PTENP1, which acts as a tumor suppressor by providing a decoy for PTEN targeting miRNAs
A subset of pseudogenes can be translated. There is a selection for preserving the length of the reading frame, which suggests (but does not formally show) the presence of a translation-dependent function of (at least a subset of) those pseudogenes. - See Xu et Zhang 2016: Are human translated Pseudogenes Functional? (paywall)
As indicated by the above, it seems likely that quite some pseudogenes have a function, which just has not been discovered yet - and that the mode of action can differ between different pseudogenes.

This is very interesting. I have added a conventional answer so that yours can be seen in context. Note that I state what the term was coined to describe, which is not changed by the fact that some pseudogenes have acquired functions distinct from encoding proteins.

The term ‘pseudogene’ was originally coined to described genomic sequences related to protein-coding genes, but which contained:

“defects… which would completely prevent the production of functional protein.”

(Quoted from review by Jeffreys and Harris, 1984.)
There are two distinct types of pseudogene:
Duplicative Pseudogenes
As their name implies, these are produced by gene duplications. As illustrated in the globin gene families, some of such duplications produce new functional genes, whereas others acquire inactivating mutations. For example a pseudogene with a premature stop codon might be transcribed and translated, but the protein would be truncated and probably degraded.
It should be noted that single mutations can, in the course of time revert, and there are examples of multi-gene families in which genes are active in some species and inactive in others. I have referred to the ABO gene family in this respect in an answer to another SE question.
Processed Pseudogenes
These arise from reverse transcription of mRNAs into DNA which is inserted into the genome, presumably by enzymes encoded by transposable elements. This may occur in any cell, but when this occurs in non-somatic cells do they become established. Hence such pseudogenes tend to be for general genes such as non-muscle actins. They are recognizable by their lack of introns, polyA sequences, and lack of promoters. Unless, by chance, they should come under the influence of a promoter they will not be transcribed and, hence, not translated.


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Splicing and “the dominance of RNA-world”
This is a paragraph from my textbook.

The significance of such complexities is now beginning to be
  understood. The split-gene arrangements represent probably an ancient
  feature of the genome. The presence of introns is reminiscent of antiquity,
  and the process of splicing represents the dominance of RNA-world. In
  recent times, the understanding of RNA and RNA-dependent processes
  in the living system have assumed more importance.

NCERT XII (pg. 111)
I am unable to understand the above sentence in bold. Can anybody explain. Thanks

I have changed the title so it is more general. This will allow better indexing and make it more likely that it is noticed by people searching the terms splicing and RNA world for general information, rather than wishing to interpret the same phrase in this book.

This is a badly-worded phrase that means nothing in the context of the paragraph in which it occurs. There is no way the reader could be expected to understand it from this awful book on its own. Normally I would not think it the role of this site to remedy deficiencies in text books. However, as this involves some interesting questions I will try to read the author’s mind.
The author probably means something like:

“splicing is a relic of the RNA world”

…although a more measured statement would be:

“the existence of self-splicing supports the idea that the current DNA/protein world was preceded by an RNA world”

The author’s use of the word “predominance” is just incorrect English. (Sloppiness or deficient vocabulary.)
An RNA world?
So what is all this about an ‘RNA world’? The author refers to this on p. 104. He states as a categorical fact what it is important to realize is only a theory:

RNA was the first genetic material…RNA used to act as a genetic material as well as a catalyst…

Why is splicing relevant to this? Some types of splicing are catalysed by the RNA itself — self-splicing — an example of an RNA enzyme (ribozyme). From the existence of these and other ribozymes it is argued that originally all enzymes may have been ribozymes, and protein enzymes only developed later, taking over most, but not all enzyme functions.
It is important to realize that RNA preceding DNA, and the first enzymes being RNA rather than protein, are two independent ideas. Although both these ideas are widely held, and I personally tend to favour them, certain scientists have argued strongly against them, as discussed by Harold S Bernhardt.

Thnx for your answer. I have accepted it. Can u plz explain that how the “the existence of self-splicing supports the idea that the current DNA/protein world was preceded by an RNA world”

@San — As I wrote, the RNA World idea postulates a stage before protein enzymes in which all enzymes were RNA. (Among other things this addresses the chicken/egg problem of protein synthesis discussed in https://biology.stackexchange.com/questions/43111/was-there-originally-a-non-ribosomal-way-of-synthesizing-proteins/43792#43792.) At a basic level, any contemporary RNA enzyme demonstrates that such a world of non-protein enzymes might have been possible. For more details you should look at the references I have included in my answer.


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Do chaperone proteins misfold?
If molecular chaperone proteins assist in the folding process of other proteins and misfolded proteins, can chaperone themselves misfold since they are also proteins? What would happen if chaperones misfolded? Can they misfold at all? Why or why not?

Someone proposed this interesting hypothesis that misfolded chaperones can misfold other proteins and/or create more misfolded chaperones. Thus prions may be some kind of misfolded chaperones.

Chaperone proteins are still proteins and they can certainly misfold just like any other. If that happens, it will either be assisted by another chaperone and given time to fold successfully or it will be destroyed. If this is happening too often and the number of chaperones drop too low or the number of unfolded or incorrectly folded proteins becomes excessive*, the unfolded protein response may be triggered and, if it does not resolve the issue and the cell remains stressed, the cell will undergo apoptosis and die.
Some chaperones, especially heat-shock proteins, may be more resistant to misfolding. This is true because they need to be able to withstand noxious conditions that denature other proteins. Not all chaperones are resistant to heat though and many are no more intrinsically resistant to denaturing.
*  It's not uncommon for a "bad" batch of proteins to be created. This can happen with a transcription error during mRNA synthesis since each mRNA molecule is read by many ribosomes. This can naturally happen with chaperones as well.

Good answer but it would be great if you can add some references for chaperones rescuing other misfolded chaperones. If you cannot find references (which, for this topic, I can understand) then you can indicate that this is your speculation.

@WYSIWYG Many chaperones are non-specific in their interactions. For some reason I'm unable to access NIH right now (my IP is blocked), but a search shows examples of non-specific chaperone-mediated folding.

https://www.researchgate.net/post/Do_the_chaperones_fold_themselves_Or_how_do_they_fold_to_such_states_which_provides_other_proteins_a_pathway_to_fold

I did a search on this topic myself but could not find any resourceful articles (researchgate is as good as stackexchange and even it doesn't have conclusive answers on this topic). So, I won't blame you.


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Is DNA a single molecule or 46 separate pieces (out of 23 chromosome pairs)?
It seems that biology books refer to DNA as 'a' molecule (implying that it is a single continuous uninterrupted double strand) ... but in those same books chromosomes are depicted as 23 separate objects (chromosome pairs) containing DNA. Are these illustrations misleading ? Are chromosomes somehow connected end-to-end or are they disjoint ? Is it a single noodle or is it 46 pieces ?

This is a trivial question the answer to which is in almost any book or article that considers chromosomes. I have voted to close on the basis that it shows insufficient research.

Unbroken strands of DNA are single molecules. So Yes, DNA is a molecule. However, the sequence of nucleotides allow for a near infinite variety. So unlike other molecules, like collagen, or water, they cannot be characterized with a unique descriptive name, other than by their sequence. I think this is the cause for confusion, because in this sense, DNA is a class of molecules, and we don't generally give them names. Each chromosome has two unique DNA molecules in diploid organisms (except in rare cases of highly inbred individuals where the two molecules might be identical). So if you have 23 chromosomes, you have 46 DNA molecules in each cell nucleus.

When a book talks about "the DNA of a cell" it is talking about all the DNA molecules which are contained in the cell.
The DNA in a cell exists as separate objects called chromosomes, each of which is usually described as a single long molecule of DNA.  (The long molecule has two strands, and coils up around many copies of special protein molecules.)
The chromosomes of a cell are separate, and do not have DNA running between them.


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What is the exact frequency of Delta brain waves during Slow Wave NREM Sleep?
I saw a TED talk about researchers playing pulsating pink noise while a test subject is in Stage 3 Non-REM / Slow Wave / Deep sleep and observing an increase in Delta wave EEG activity. This seems to indicating that the burst frequency of the pink noise is matching the dominant frequency of the Delta waves. (Skip to 5:00 to hear a sample of the sound)
My question: While a spectral analysis shows a range of brain wave frequencies, and many sources define a range such as "0.5-4 Hz", I'd like to find a more precise dominant frequency of Delta waves.
The video inspired me to write my own small computer program to make my laptop play a similar pulsating pink noise pattern on the table next to my bed last night. I arbitrarily chose 1 Hz as the pulse frequency, and the following pattern:
30 min silent (to give me time to wind down and fall asleep)
  60 min sound
33 min silent
  54 min sound
40 min silent
  45 min sound
49 min silent
  37 min sound
57 min silent
  30 min sound
30 min silent

So roughly 5x 90-minute sleep cycles with an increasing ratio of silence to noise to mimic the ratio of REM to NREM as the night progresses. I've read that REM is characterized by un-synchronized brain waves and NREM is where you see large amplitude synchronized Delta waves which the sound experiment is trying to help stimulate. Tonight I will wear my FitBit bracelet with heart rate and sleep stage tracking to see if the readings match the sound schedule.
Bonus Questions:

How credible is the hypothesis that playing sounds can affect the quality of sleep?
Would a different sound than pulsating pink noise work better?
Does the phase matter?
Also, I couldn't help but notice that Deep NREM sleep seems to be the only time you see a single large amplitude frequency dominate on EEG and it's suspiciously close to the average Resting Heart Rate of 60 bpm...are Delta waves and heart rate related?

don't try to mess with your sleep.  all phases of sleep have important things going on in them.

Periklis Y. Ktonas and Atul P. Gosalia performed such an analysis. It was published in 1981 under the heading "Spectral Analysis vs. Period-Amplitude Analysis of Narrowband EEG Activity: A Comparison Based on the Sleep Delta-Frequency Band"
The bins were quite wide but their analysis showed peak power spectrum moved between 0.84 and 1.96 Hz at different times.
I think the paper would serve you well, as it highlights the difficulty in achieving what you have set out to achieve. The frequency is not constant, even over short timescales. It depends for the most part on a balance between the intrinsic, basal polarity of thalamocortical neurons, and the effect of synchronising, inhibitory input from the reticular nucleus. The latter is in turn subject to cortical feedback. There are huge numbers of neurons involved. The period between bursts, and the number of action potentials per burst, is quite variable.
Perhaps it might be possible to set up a device that alters the round in real time, based on the EEG measurement.
With regards to your 'bonus' questions:
(1) The video posted does show an effect on the thalamic rhythm, which is surprising, as it had been thought that in deep sleep, sound has no effect on the thalamocortical circuit, since it is gated at the thalamus. This shows the plausibility of the hypothesis. However, the video does not provide any evidence that this alteration in rhythm is beneficial. It is possible that it is not and this possibility should be eliminated.
(2) Clearly the sound has an effect on the rhythm, so it seems entirely plausible that there is an optimal sound to maximise the effect.
(3) It will be hard to organise the phase, given the continuous, rapid shifts in period, unless done in combination with EEG in real-time.
(4) I am not aware of any research attempting to correlate thalamic rhythms with heart beat, although it would be quite easy to do. However it is highly unlikely there is a correlation, since the thalamocortical period has a lot of variation moment to moment, whereas the heart rhythm does not. Also the thalamocortical rhythm is generaly somewhat faster.

Thank you for the excellent response (even if I'm a little disappointed to hear it). What do you make of the part of the TED talk where the presenter showed EEG readings that did in fact respond to sound?

OK, I have to admit that I haven't seen that effect before. There is a clear response to the sound in the wave. My statement that sound "has no effect on the thalamus" is incorrect, so I will edit it. But I think what you should look for is evidence that this artificial alteration of the rhythm is beneficial. You could be having the opposite effect to that intended. It would be interesting to compare the effect on rhythm shown with the effect of the sound of wind blowing through trees, or water babbling down a stream, so if you get that far, do share your results ;-)

Well, strictly, you should look for evidence that it isn't beneficial, of course ;-)

Heh yes well causality and health benefits are notoriously hard to prove - plus I don't have an EEG.  So far I've lowered the pink noise pulses to 0.8 Hz and tried it for a few nights. While it's impossible to say whether I've felt any different the next morning due to placebo, I do think I had/remembered more dreams which is surprising since SWS is supposed to be dreamless.  The other thing is that on nights where I have a hard time falling asleep the sound can be distracting, like disembodied breathing. On normal nights I'll wake up and notice it playing but fall back asleep without issue.

I thought you might be interested in this, a Nature news feature last week: https://www.nature.com/articles/d41586-018-02391-6


text:
Why have plants evolved to photosynthesize glucose instead of another molecular compound?
I think this question can be broken down into two sub-questions:

Why do plants produce $C_6H_{12}O_6$ as opposed to another molecule following the formula of $C_nH_{2n}O_n$? Why not $C_8H_{16}O_8$, $C_4H_{8}O_4$, or any other of the many possible variations? Does it likely have something to do with stability or some other property that glucose has that many other variations on the formula do not?
Why have they evolved to produce a molecule following the formula $C_nH_{2n}O_n$ at all? In short...why carbohydrates as opposed to another family of compounds?

My assumption is these are questions that have been researched extensively in biology and evolutionary biology and have at least tentative answers.
I'm looking for either your best hypothesis or a currently popular hypothesis within the relevant scientific disciplines. I understand there is likely no "definitive" answer, but probably at best pretty good hypotheses.

Evolution had already worked out how to break down glucose for energy...why reinvent the wheel?

I hope you get an interesting answer, but be aware that while "why" questions are easy to ask they are very difficult if not impossible to answer. Maybe there were multiple metabolisms and the glucose based one was better. Maybe glucose based metabolism happened to occur first and now we are stuck with it because it is too central to change.  Assume you came up with a reasonable hypothesis — how would you test it?

@tyersome Perhaps you couldn't test it. I've amended the post to ask for "your best hypothesis or a currently popular hypothesis within the relevant scientific disciplines." I understand there is no "definitive" answer to this and I hope this addition to my question makes that clear.

Plants do though! C8H16O8 is found in bay leaves and C4H8O4 is found in rhubarb

This is a brief answer (for me) to point out that:
Your question is not really concerned with photosynthesis but is actually about the choice of the carbon constituents of living cells.
First you talk about photosynthesis as if it is a single process, however it is two separable processes:

The Light Reactions convert solar energy into chemical energy (in the form of ATP and NAD(P)H).
The Dark Reactions use the chemical energy to reduce carbon dioxide and elaborate it to more complex molecules.

Photosynthesis is so elaborate chemically that it clearly was not the first process by which living organisms managed to convert environmental energy into a usable form. So the question becomes:

Q. Why is chemical energy trapped by living organisms used to make
  compounds such as glucose 6-P?

and giving what may at first sight seem to be a frivolous answer

A. Because glucose 6-P and its precursors and metabolites were suitable molecules for building the structural components of cells, that had arisen early in evolution.

So the question becomes:

Q. Why did the structural components, energy storage, genetic information
  etc. of cells evolve to employ the particular molecules that we find
  today, most of which can be formed from glucose metabolites?

And that is a very broad question about a very speculative area of chemical evolution, which cannot be summarized here.
In general one would imagine that the answer is related to the carbon components available in the environment and the possibilities of chemical transformations. However the trap is that one ends up arguing that things are the way they are because that was best. Which is all very well until one discovers dirty little secrets such as the fact that archaea evolved different chemical constituents for their cell membranes.
Footnote
My first degree was in chemistry. Since becoming a biochemist/molecular biologist I have almost never talked in terms of overall chemical formulae of molecules in the manner of the question. It has seldom been a useful way to approach biochemical reactions or intermediates. What has been more important is to look at their structures and ask how they lend themselves to their functions or interconversions.


text:
How does antagnostic coevolution work in ducks?
I recently learned that in ducks, the penis and vagina have coevolved: the vagina of the female ducks gets dead-end sacs and clockwise coils; the penis of male ducks become longest and its morphology changed to adapt to the female vagina. [1] This antagnostic coevolution happened due to the evolutionary arms race between male and female ducks.
This seems counter-intuitive when we think about natural selection. Indeed, if female ducks are forcibly copulated, they are more susceptible to reproducing themselves and sharing their genetic traits.
From  [2], it appears that only 3% of forced copulations results in fertilization. If this is the case, why has the male phallus evolved this way? Indeed, it does not appear to me to be a good evolutionary strategy.
If [1] and [2] are correct, I would think that the duck vagina and phallus shouldn't have coevolved that way. What am I missing?
[1] Brennan, P. L., Prum, R. O., McCracken, K. G., Sorenson, M. D., Wilson, R. E., & Birkhead, T. R. (2007). Coevolution of male and female genital morphology in waterfowl. PLoS one, 2(5), e418.
[2] Burns, J. T., Cheng, K. M., & McKinney, F. (1980). Forced copulation in captive mallards. I. Fertilization of eggs. The Auk, 97(4), 875-879.

Your question is unclear what don't you understand, preferential mate selection? That male and female genes can have an antagonistic relationship?

@John I don't understand why phallus AND vagina evolved that way. According to me, if females are forcibly copulated, their genes should spread (so no dead-end sacs vagina). But if forced copulations don't result into fertilization, it is a bad reproduction strategy for males and they should evolved in a non-rapist species. However, it is not what we see and that is what I don't understand.

There is a difference between spreading your genes and spreading your genes in the most effective way, it is the same reason animals are picky about mates, A male who mates with a female can go find a different female the next day, an impregnated female now can't mate even if better males are available.


text:
How does the helicase enzyme break the hydrogen bonds between the strands of DNA?
I know helicase breaks the hydrogen bonds between the strands of a DNA, but how is this done?
Does it put an ion between the strands of the nucleic acid so that the bond breaks apart itself or is there some other mechanism?

Welcome to SE Biology. I have edited your question for two reasons. We discourage extraneous material and chat in questions — keep to the facts. If you want to add personal information, the most relevant is what level your knowledge of the subject is already. This is not my field, but I found a 2006 mini-review of the topic which indicates that there are many different helicases and their mechanisms of action are not simple to summarize. Someone may be able to do it for you, however.

This is indeed a broad question. For a detailed mechanism you should read a structural biology paper on this topic. This subject is complicated to explain in a site like this (also requires good knowledge of biochemistry and biophysics). A very short answer would be that helicases use energy of ATP hydrolysis to separate the DNA strands.

Im not sure if there is a decided helicase mechanism but the ‘backbone stepping motor’ model has been proposed for
helicase translocation and unwinding. Helicases contain two domains that are analogous to a set of ‘pincers’ (motor domain), when ATP is present, there is only a distance of two nucleotides between the
pincers and so they are closed, whereas when ATP is absent, there is a distance of three nucleotides between the pincers and so they are open. The motor domains interact with the
nucleic acid through contacts between threonine residues on the pincer terminus and phosphoryl oxygen on the nucleic acid. ATP binding weakens these interactions, allowing a pincer to move one nucleotide closer to the second pincer. A third domain (D3), that is part of the helicase but not involved in the binding of ATP, also interacts with the nucleic acid using a threonine residue. As the motor domains move along, tension builds up between the motor domain and D3 and after the motor domain has moved three base pairs, the protein contracts like a spring, pulling D3 toward the motor domains, disrupting the DNA in between. The structures responsible for prying apart the DNA are called “pins” or wedges”, which act as a physical barrier between the two strands of nucleic acid, prying apart its structure. The single
stranded regions are stabilised by helicases as well as other proteins such as single stranded DNA binding proteins, which prevent the reformation of the double stranded nucleic acid.
For more information and good images see: “Translocation and unwinding mechanisms of RNA and DNA helicase”

It's good to have more people answering questions in this area, but as you are a new member of this list, allow me to point out an important feature of answering questions on SE. This is that answers should be supported by external sources — reputable scientific articles, either in print or online (preferably with links). The reason for this is two-fold. 1. Without it it is difficult for the poster or others with the same question to know whether the answer is correct. 2. It is helpful for anyone wishing to learn more about the topic. Could you add references to your answer, please.

Sorry I put the name of the paper at the end which is in my opinion a really good article but I'll add the doi


text:
Do animals exist (for example ostriches, chimps, etc.) that develop the need to mate with humans if they are soley raised and socialized by humans?
I just watched a German talk show "Nachtstudio" with the title "Die Graugans und der Mensch" (Gosling and People) about the legacy of the famous ethologist and Nobel Prize winner Konrad Lorenz (https://youtu.be/hLkWhGieZvQ). All the participating guests were former students of Lorenz. One statement in the show made by Bernd Lötsch amused me.
At the point where the conversation was about the famous experiment of Lorenz with geese,  Lötsch said that Lorenz was lucky that he had selected goslings for his experiment. He continued by saying that if he had chosen ostriches, it would be likely that the ostrich would have tried to mate with him once it had reached maturity (Lötsch 1988).
Amused by his statement and without any deeper understanding of biological theories (I'm a physicist by training), I would like to ask for critical reflections on Lötsch's statement. I would also appreciate hearing about any studies which examine hypotheses such as this.

Dogs some to mind. But the real issue is proving it, A lot of animals aren't terribly picky about mates.

Content warning: frisky kākāpō ahead https://youtu.be/9T1vfsHYiKY


text:
What type of flask should I use to culture NTERA2 embryonic cancer stem cells?
I'm just starting my MSc research and I am in the process of making a list of equipments/consumables to order. Is there a specific flask in which I can culture NTERA2 (NTERA2/D1) cell line?

I just use regular TC-treated Petri dishes and flasks - nothing special.

I found a protocol by ATCC for NTERM2 cells, and it didn't mention any specific flask, so any cell culture flask would do. Since ATCC is basically a cell culture bank I trust that their protocol is valid.


text:
Why ml scale blood retrieval is required to run a blood test?
Substances found in blood are present at microscopic scale and tend to be invisible to the unaided eye. Why is a whole vial of blood (at ml scale) is required to assess the presence and concentration of substances, given that the modern equipments and testing is becoming more and more sensitive and efficient?

Can you please specify what kind of blood test you are talking about. And what is "so much blood"?

@Chris I would think that in any blood test you're looking for the presence of microscopic molecules, and thus you'd only need a very small drop of blood.

In fact a lot of tests are not done using a microscope. And besides that, you can not see molecules in the microscope. You can see cells. Typical amounts for blood tests are 4.5 or 9 ml which is not very much. Enough to handle and prepare the sample and to repeat it, if something goes wrong.

@Chris So is it a question of technology/affordability? Are we capable of obtaining the information from a very small drop of blood?

That depends on the type of test you want to do.

@Chris How is it that there exist tests that look for microscopic particles that can't be done with a drop of blood?

Because some of these tests need some amount of volume to properly work. (Automatic) Handling is also not getting easier when the volumes are getting very small. You want to have reliable and reproducable measurements.

@Chris What I'm asking is why these tests need some amount of volume to work.

It might be better to consider the sampling technology, economic and logistical issues with this question as well as the tech behind the tests.
First, some tests still will want a few milliliters of blood - e.g. cell counts for specific cell types.  Then there is the need to create and stock many different kinds of sample collection devices and train the collection centers to use them effectively- the industry won't be wanting to completely retool whenever the volume requirement for the assays changes.
Mainly, since the expense of collecting and shipping a few milliliters of blood is pretty much identical to doing so with a few microliters of blood, what has happened is that the tubes are used to do multiple assays with excess included in case an assay has to be redone.
Probably all this blood currently collected is not necessary at all.   I expect that the cost of changing all the blood collection systems and protocols is not worth the cost of collecting the exact minimum amount of blood needed.  The benefit to the patient or the lab between collecting 3-5 ml of blood and collecting 50 microliters of blood to be shipped off for lab analysis is probably close to zero.
Having more blood than you need does not hurt the lab either should they need to repeat the assay or when you need to use the sample for more than one different test.

So would it be possible to design a device that runs any blood test on a small drop of blood?

In many cases it would and people are working on that.  Microfluidics is taking the biomed world by storm.  That being said, there are potentially thousands of assays that are or will be devised for the market.  how many of them will be run out of a smartphone, time will tell.

Could you expand a little more on how blood tests work and why it's easier to do them with more blood?

Sorry i'm not being clear.  I've added one paragraph above to summarize...

Could you explain how blood tests actually work? Like do they look at it under a microscope or something? I think if I understood how they test blood it'd help me understand why it's useful to have more of it.

I have a doctor's order for a lab test here - there are scores of tests done with blood.  some of them stain cells and then count them under a microscope, others are chemical analysis of the plasma, others apply antibodies to cells in the blood, others sequence the DNA of cells in the blood.  There's really quite a variety - that sort of deserves its own question or may be too broad for a single question.  some require little or no sample tho.

One important point to be added here is that the tubes are usually vacuum / low pressure, to get the blood flowing into the tube.   This could be very hard to manufacture on a much smaller scale. And something else: many tests don't require too much sample, but standard equipment is built for a bit of excess volume (for example a HPLC accepts 1 mL tubes, while probably only 1-10 uL is actually injected). It's also efficient to use the same collection tube, whether you're doing one test or 20.

If they're collecting multiple tubes it's also mostly because different types of tests are done. https://www.bd.com/vacutainer/pdfs/plus_plastic_tubes_wallchart_tubeguide_VS5229.pdf

@shigeta brings some other interesting reasons, but I think the main problem with small draws is lack of representativity.
I suspect you are hoping that something Theranos "nanotainers" will replace today's blood draws. The fact is, the first drop of blood is not the most representative for the whole blood. For example, drops of blood collected from finger pricks are not very similar. if they differ between themselves, they are likely to differ from the rest of the blood. This variability is probably why Theranos tests were shown to be quite variable.
For some tests, it might not matter. Home fingerstick tests for blood sugar at home are generally acceptable, but even those come with a warning that results are somewhat inaccurate. For others, such variability cannot be tolerated. They may be too expensive or too urgent to allow repeats in case of a borderline result. They may be so scary that false positives must be avoided as much as possible. In all these cases, the tests must be run in the most representative conditions.
More blood collected is essentially averaging multiple drops. Many  tests are done on very small sample of blood - smaller than a drop. Drawing that sample from a bigger pool of blood makes the readings more representative for the rest of the blood.

The problem with Theranos is this they results are obviously not accurate and that they lost their testing licence over that.

@Chris I don't know what are you implying with your comment. I think I said just that, and suggested a reason why "results are obviously not accurate". Are you suggesting the problem is not caused by the tiny blood volume, but by something else?

From the few, which has been published about this, it seems like this. There are numerous reports of customers which say that by far more blood was drawn than announced (the "needle prick").

There are hundreds of tests that exist but many require different technologies so getting them all out of one drop is nigh impossible.
For a large fraction of your average chemistry/immunology blood tests, the blood has to be transported in a way that keeps the blood liquid so the collection tubes have anticoagulants in them. The analysis involves pipetting microliters of plasma into a cuvette where different reagents are added and the ensuing chemical reaction is monitored by a spectrophotometer which detects various chemical products by select wavelengths that are absorbed or emitted. This requires the red blood cells to be removed before the sample can be analyzed(they would block the light), so the collection tubes have a gel at the bottom and the sample is centrifuged before analysis so that the blood cells get buried in the gel and the analyzer probe can then extract just the clear plasma above it. Each assay has to be run in it's own cuvette otherwise the reactions would all be mixed up and it wouldn't be possible to quantify the assays separately. Using this approach we can currently run about 50 quantitative assays out of a ml or two of blood. Some assays require different kinds of tubes for various reasons so they may collect a red top and a green top tube when otherwise a single tube would do, and, as others have said, some excess is collected to enable reruns or add-on tests that your doctor may specify after seeing your initial results. If you only collected a small drop of blood (like is used in hand-held blood-glucose meters), you wouldn't be able to get it out of the collection tube and into the multiple reaction/measuring cuvettes.
There are technologies that detect e.g. DNA on a chip that could conceivably detect multiple viruses and things from a single drop of blood, but they fundamentally rely on some underlying chemistry/physics that would probably make them single use if connected to a phone.  While they are very specific, that tends to make them good for detecting things qualitatively (do you have HIV or HEP-C?) but probably won't make them good for quantitative test (how much potassium or glutamate do you have in your blood). And trying to combine that with e.g. counting red and white blood cells is unlikely at this point. But technology is constantly improving.

Hi Gary. It would be great if you can add some supporting references. Wikipedia links would also do but research articles/reviews would be the best.


text:
What are the genus and species name of different breeds of dog?
Can you refer me to a good source containing the genus and species name of different breeds of dogs?

Why in "Can any species be bred selectively/engineered to become as diverse looking as dogs?" is link provided to "not scientific" list of dog breeds?

Why in "Can any species be bred selectively/engineered to become as diverse looking as dogs?" is link provided to "not scientific" list of dog breeds?

All the different breeds of dogs - from Irish setters to greyhounds - are all part of the same species, canis lupus familiaris. The common, domesticated dog is actually a subspecies of the grey wolf. The different breeds do have different genetic characteristics (just as humans have, say, different eye or hair colors), but they're a all one and the same. The different names for different breeds are not like the scientific classifications of organisms via domain, kingdom, etc. They're just our choices.

References:

http://www.vetinfo.com/scientific-name-for-dogs.html
https://en.wikipedia.org/wiki/Dog_breed#Description
https://en.wikipedia.org/wiki/Subspecies_of_Canis_lupus
http://www.choosing-a-dog-made-easy.com/dog-types.html

All breeds of dogs are members of the same (sub) species: Canis lupus familiaris. "Breeds" of dogs are not scientific designations but are collections of traits recognized as unique by different breeding organizations. As such, certain breeds are recognized as unique in some organizations do not exist in others (see here for examples).

Ahh, didn't see your answer. Sorry about that.

@HDE226868 Don't be sorry. Multiple answers are encouraged, and improves the quality of the site.