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How do scientists discover a new antigen and its epitope?
I've found some database on the internet that list all discovered antigens and their epitopes.
So how do scientists discover a new antigen? Do they try to inject them into the body to see if it causes an immune response or not? And finally if it's an antigen, how do they know their epitopes?

Okay, you have a few questions building on top of each other (rephrased the questions for clarity):

How do scientists discover a new antigen?

There are multiple ways to this, which are applied for different purposes.
In order to discover a natural antigen, which is recognised by an antibody normally produced by the immune system, one would first have get hold of this specific antibody. This would be an approach to reproduce or understand the effective response of the immune system against a pathogen (e.g. a virus).
In order to get hold of the antibody (and ideally the coding DNA sequence for it), researchers have to use the pathogen, or parts of it and find the antibodies (or B cells) that bind to it. To do this the pathogen (particles) could be fixed to a column and after running blood through the column the respective antibodies and B cells will remain in the column. Then the DNA of these cells can be sequences, or the antibody can be further purified.
In most cases however, scientists want to find a not-yet existing antibody against an antigen, which leads us to:

Do scientists try to inject antigens to the body to see if it causes an immune response or not?

Yes, this is done - but only with animals (mostly rats, rabbits & goats). Polyclonal antibodies can be extracted directly from the blood of these animals, but most often monoclonal antibodies are needed for research or medical purposes. The process required for these is much more complicated, but leads to a cell lines which can then be used to produce the desired antibody in greater quantities.

How do scientists know the corresponding epitope to an antibody?

There are multiple ways to find the exact epitope of an antibody, all of which are commonly described as epitope mapping.
The most common methods are based either on site-directed mutagenesis of the antigen to see which positions (amino acids) are crucial for binding of the antibody, or on peptide fragments of the antigen, which can still be bound by the antibody.

Great answer! Thank you very much. Since "the DNA of these cells can be sequences, or the antibody can be further purified.", we can know its epitope by analysis its DNA or use the purified antibody for epitope mapping.

"The most common methods are based either on site-directed mutagenesis of the antigen to see which positions (amino acids) are crucial for binding of the antibody" . I've never known about this, let me search for it. Thank you very much!

@joe In most cases you would use the purified antibody for epitope mapping. There are people working on computational epitope prediction, but I'm not sure how good/reliable these predictions are so far - this seems to give a recent overview

very responsible answer, thank you very much for sharing your knowledge, keep rocking!

I would like to just add to Nicolai answer.
What is an antigen ?
First, and Nicolai said this, but I just want to make it clear, an antigen is anything that antibodies bind. That is distinct from and immunogen which is a type of antigen that causes your immune system to produce antibodies. But an antigen does not necessarily have to be an immunogen.
Peptides, sugars, nucleic acids and lipids are all common antigens, but peptides are probably what you would be most familiar with. Usually, most sugars and lipids have a hard time producing an immune response on their own and generally are coupled with a protein (peptide). This makes sense because your body naturally produces lots of sugars and lipids and if you made antibodies to all of them, it would end up attacking itself.
How is an antigen discovered?
There are two ways to approach this.

Antibody First Approach

Let's say a person get's infected with some unknown virus but ends up surviving. The next step would be to do two things:

Culture the virus so scientist can study it in the lab. You need
to culture most virus so you can grow an unlimited amount in vitro.
It would be a really tough task to go out and naturally find all the
virus you needed to study.

Genotype the virus. It is necessary to know the viral genome so we can manipulate the genes and see what their effect is.

We can start making changes of the virus changing various components of the genome. We could see how that changes binding to the patient's serum.Since the serum contains antibodies that will bind the virus, the serum will often neutralise or test positive for binding antibodies. Now if we change gene A from the virus and the serum still binds/neutralises, we can assume gene A is not the antigen which made an immune response in the patient. If gene B is mutated and the serum stops binding, we can assume gene B is the antigen of the unknown virus.

Antigen first approach

If we only have the virus and don't have an infected patient, then we would have to inject it into model organisms to find out the antigen. However, since we know an incredible amount of viral species we can probably make a best guess on what the antigen component of the virus is.
For instance, in 2012, when a patient fell ill, they sequenced a virus in them which was found to be a close relative to Coronavirus. Since they know that Coronavirus primary antigen is its spike protein, they rightly assumed that the gene that was closely related to the spike protein of the unknown virus was also the primary antigen. That virus turned out to be Middle East respiratory syndrome coronavirus which the main antigen is the spike protein.

Another great answer, very detailed, thank you very much!


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Does terminology for changes in membrane potential refer to additive or multiplicative change?
Is the membrane potential just the number of mV, or is it to what extent it differs from 0?
For example: If the mV goes from -40 to -60, can you say that:

The membrane potential decreases, because the number of mV decreases (from -40 to -60)
or
The membrane potential increases, because the difference to 0 increases (from 40 to 60)?

Short hint: It is same as electric potential, as we study in physics. with the same unit Volt, with magnitude adjusted with metric prefix (milli, micro, nano, pico etc), with positive ($+$) or negative ($-$) value. The concept has been taken in Electrochemical potential

Note to others: this question appears to be about terminology rather than the biophysics behind the membrane potential.
When the terms "increase" and "decrease" are used relative to membrane potential, they refer to additive changes in potential, not to multiplicative change or effects on absolute value. The standard is to relate the potential inside to the potential outside of a cell (so a negative potential means the inside is more negative than the outside; potentials in biology are always relative, just like in physics).
Therefore, a membrane potential decrease means that the value of the potential becomes more negative, and a membrane potential increase means the value of the potential becomes more positive. The changes on the absolute value of the potential depend only on where you start from.
Other terms that are more clear to use are hyperpolarization and depolarization, where hyperpolarization always refers to the membrane potential becoming more negative than rest, and depolarization refers to the membrane potential becoming more positive than rest. Repolarization is also used, particularly in the context of action potentials, to refer to voltage changes in the direction of hyperpolarization when the cell is currently depolarized.

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Troubleshoot bacteria fixation for SEM
I fixate bacteria on titanium coins for 1 h i 2.5 % Gluaraldehyde. Then wash 3 times in ddH2O. Then 10 min in each solution of Ethanol 10 %, 30 %, 50 %, 70 % 90%, 100%. Finally soaking in HMDS in 15 min, then take out the HMDS and let dry overnight. Sputtercoat with Ag/Pd. I know I have bacteria on the titanium surface from the beginning but I dont see anything in SEM. What am I doing wrong?

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


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How did scientists discover HIV?
Imagining that we're now in 1983 (when HIV was discovered), there were no modern machines at that time to sequence massive genome extracted from blood. There was a strange disease and no one know what caused it, it's a virus or a bacteria or something else... So how did scientists find out HIV at that time?
-- Update: I just think that they extracted RNA from blood of those patients who have the same symptoms and using electrophoresis to find out if there was a large ARN fragment exists to indicate that they was infected by a virus, is that true?

See And the Band Played On for a docu-drama retelling of the story, where epidemiology plays an important role. Well worth the watch.

Not to minimize Iayork's fine answer, but the same way they discovered polio was a virus, smallpox was a virus, chickenpox was a virus, Infectious Mononucleosis was a virus, Influenza was a virus, etc., etc.

HIV was identified as an infectious disease through classical epidemiology, and the virus was identified through classical virology.
I won't get into the epidemiology, but briefly it went pretty much as you'd expect -- a cluster of symptoms were identified, patient characteristics were analyzed, the contagious nature of the symptoms were recognized, all through standard approaches of patient tracking and so on.
As for the virus identification, that was long before modern molecular techniques were available.  It was even before PCR was commercially available!  So the techniques that were used were those of classical microbiology.
It seemed most likely that the agent was a virus rather than a bacterium (though every possible angle was covered), and just about every virologist tried looking for their favorite agent, but retroviruses also seemed like logical candidates and several groups tried isolating infectious agents from the blood of AIDS patients.
The two groups who were most successful were those of Luc Montagnier and Robert Gallo.  There turned out to be a lot of politics and personalities involved and I won't get into that.  Here are some comments from Montagnier summarizing the story:

There were only a few patients with this disease in France, but Gallo's idea that a retrovirus was the cause had already crossed the Atlantic. His idea was disseminated by a small group of clinicians and immunologists led by Jacques Leibowitch and Willy Rozenbaum. At the end of 1982, Françoise Brun-Vezinet, a former student of mine and a member of this group, proposed that we collaborate to discover if a retrovirus was the cause of this disease, now called AIDS.
We were ready to start because my laboratory was equipped to hunt for lymphotropic retroviruses in human T cell cultures.  ... On 3 January 1983, Françoise Brun-Vezinet obtained a lymph node biopsy from one of Rozenbaum's patients, ... I minced the lymph node, dissociated the fragments into single cells, and cultured the T lymphocytes with interleukin-2 and antiserum to human interferon. Fifteen days later, Françoise Sinoussi (by then Barré-Sinoussi) found the first traces of RT in the supernatant of the lymphocyte culture, indicating the presence of a retrovirus.  ... A few months later, I received a blood sample from a young hemophiliac (LOI) with full-blown AIDS, and blood and lymph node samples from a young gay man (LAI) with advanced Kaposi's sarcoma. The LAI virus could be isolated from the patient's blood cells and grew very quickly in the patient's cultured T lymphocytes, killing them as well as killing T lymphocytes from blood donors.
New evidence that this strange retrovirus was the cause of AIDS came from our team in the fall of 1983 and the winter of 1984 (7). We observed a high frequency of antibodies against the virus in lymphadenopathy patients, and noted the favored tropism of this virus for CD4+ T lymphocytes. Our results were still controversial, however, and we had difficulty in obtaining the funding needed to better characterize the virus and to develop a blood test. The tide only turned in France when Robert Gallo and his group in the United States made a similar discovery. In the spring of 1984, Gallo published more convincing evidence that HIV causes AIDS ...

--A History of HIV Discovery
Gallo's approach was similar -- focused on isolating replicating virus, more than performing the molecular biology that's become standard in the meantime.

Dr. Gallo would want his name listed first, in your list.

Man, the politicking was so unpleasant and tedious. I really don't want to relive that.

There is a brief, relatively dispassionate, and from my memory reasonably balanced summary of the politicking in HIV, HPV Researchers Honored, But One Scientist Is Left Out, if people don't know what we're talking about

@iayork gah it's behind a paywall for me sadly.

@DRF The fine print for "Science AAAS" says research is free one year after publication if you register.  The paper was published in 2008.  I have not tried but you should be able to read it if you are willing to register

@TonyDallimore Yeah I was hoping so, unfortunately I'm guessing they count this as an op-ed or whatever so it's not accessible even after registration. Still thank you for the link. I think I probably have the hard copy some place.

Just to remind people that science is hard (and all about making mistakes), it could be worth giving examples of one or two of the incorrect claims about the aetiological basis of AIDS (at the time and by reputable scientists, I mean, not modern denialist stuff). For example, there was a paper in the Lancet in 1983 suggesting it could have been caused by African swine fever virus (http://www.thelancet.com/journals/lancet/article/PIIS0140-6736%2883%2991345-4/abstract), which is... pretty different, to a virologist (to put it mildly).

...although this may not be the best example; the Teas theory got a pretty cool reception at the time, as far as I can tell (this was all rather before my time).


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How many genes are needed for a living organism?
I am interested in this question as I'm doing research into early life on earth which is believed to have been single-celled. Therefore, by extension, it seems only logical that the first life would be as genetically simple as is possible, therefore I present the above question.
How many genes / pairs of AA would be the bare minimum for something to be considered alive and function as an organism.

Hi there. You're right the question is the same but the answer given doesn't link any studies and i think it's also possible that the date is outdated.

Related wikipedia articles: Constitutive gene, Housekeeping gene , Minimal Genome and repressible system. Though they are not same thing, but they are related concepts.

Check out this answer: https://biology.stackexchange.com/a/56363/6307


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Understanding what passes through and doesn't pass through the plasma membrane
I have difficulty in understanding the reason why certain molecules can pass through phospholipid bilayers.
Firstly, I understand that the outer layer of the lipid bilayer is hydrophilic - my understanding is that they "like water" and can interact better with water.

Bilayers can absorb hydrophobic substance like N₂ and O₂.

Does this mean - because the hydrophilic surface are capable of hydrogen bonding - that's why they are able to absorb hydrophobic substances like F , O and N ?

They can absorb non-polar molecules.
They can absorb small uncharged molecules like H₂O and CO₂.

I'm not sure of the reasons behind 2 and 3 ...
And of course , vice versa ... (what can't pass through the lipid bilayer easily).
Any help would be appreciated!

Related: Why lipophilic molecules can pass phospholipid bilayer, in spite of 2 hydrophilic layers?

Great questions! Your 3 questions can be answered in 2 parts:
1. How do small, uncharged gasses (ie: O₂, N₂, CO₂) diffuse through lipid bilayers?
First it's important to clear up some terminology: Absorbing a compound isn't the same as being permeable to that compound. If you say that a compound is absorbed (or partitions) into a bilayer, you're assuming that the absorption of the given compound by the bilayer increases the entropy of the system (and is thus energetically favorable). For example, lipophilic compounds partition into lipid bilayers because of the hydrophobic effect; by partitioning into the bilayer they break a number of hydrogen bonds and thus increase the disorder of the system.
Small, dissolved gasses like O₂, N₂, and CO₂ are not absorbed into lipid bilayers, they simply diffuse through passively because of their small size and because they are non-polar.
Water is also able to passively diffuse through a lipid bilayer even though it is polar. We might think it should be fairly rare for a polar water molecule to pass through the hydrophobic center of a lipid bilayer, but typically living cells are found in aqueous environments, where concentrations of water outside the cell are extremely high, so this does occur at biologically relevant rates. In fact, the passive diffusion of water in and out of cells is so important that many cells have developed special transmembrane proteins to facilitate the passage of water in and out of cells (most notably aquaporins and pressure-gated channels).
2. How do non-polar molecules pass through lipid bilayers?
This is answered in the related question posted in the comments section of your question. Briefly, it has to do with the same electrostatic problem I mentioned above: Though there is an energetic cost for non-polar compounds to pass through the hydropilic layer of a lipid membrane, in most cases the partitioning of the compound into the membrane still raises the overall entropy of the system (due to disruption of the hydrophobic effect), making it an energetically favorable process.
It should be noted that for the most part, polar compounds do not spontaneously cross cell membranes because of the hydrophobic region of the lipid bilayer. When passage of these compounds into or out of the cell is required for life, cells typically produce transmembrane proteins which can act as either active or passive transporters to allow these compounds through.

Good effort, just a couple of points. It is true that there is some spontaneous water exchange across membranes, but not because water molecules are small, rather because the concentration of water is very high. And still water exchange over membranes is limited, that's why cells have aquaporins. For (2), I think you should rather emphasize that most polar compounds do not cross cell membranes spontaneously. (That's of course the reason for having cell membranes in the first place, to keep solutes inside cells.) Transport proteins are required to move polar metabolites across membranes.

@Roland, good points, I'll fix my answer to reflect them. I had decided not to mention larger polar compounds and transport proteins since they weren't mentioned the original question, but I can add some detail for clarity.


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Identifying a spider from coastal Virginia
A spider recently put up a web in my room in coastal Virginia, USA (on the left in the photo).
Rounder/taller body than most species I've seen. Dark brown, not quite solid-color coloration. If laying flat, it looks like its body would be about the size of an American dime. Tends to hang with its underbelly pointed upwards, and the times I've watched it feed it has never attempted to wrap prey in silk –- instead, it immediately eats and discards them.
My best guess from what I was able to find online was Araneus diadematus, but the coloration on all the examples of that species I can find seems much more varied than what I'm seeing, and I'm not particularly well-versed in spider identification, so I'm not sure.
The spider on the right was new this morning, I'm less curious about it and presume it was just a male of the same species.

Please provide some close-up photos if possible. A Photo of the abdomen and the back are preferential. Thanks

@theforestecologist Not sure I can get much closer without disturbing the web, but I'll see what I can do when I get home tonight.

These are very likely one of the common spiders that gets called House Spider, but this variety is one of the comb-footed spiders; the Theridiidae.  They're sometimes also called Tangleweb Spiders or something along those lines.  They make those messy webs, and hang upside down just as you show.  You can tell these guys aren't Araneus or one of the other Araneid orbweavers, because they're not hanging vertically in an orbweb.  This particular spider is probably the very variable and common Parasteatoda tepidariorum, and the smaller one is, as you guessed, a male.  They will share the web for a day or so until he mates and moves on.  You should be aware that the related Black Widow has this same general body shape and habit, and may be stripy and have banded legs like you see in the photo when the females are young.  I suspect that was why TFE was asking for better photos - although you probably would have noted the red hourglass before if that was the case.  I'm inclined to go with P. tepidariorum, for two reasons: Latrodectus generally (but not always) are sensitive to disturbance, where the common House Spiders don't seem to mind, and the abdomen of the female seems to be a little more randomly patterned (as best we can see) than I would expect for a Latrodectus.
Here's a photo of P. tepidariorum with a snack:

https://bugguide.net/node/view/6919/bgimage

Very informative answer, but again please provide some evidence/support/citations/etc to back up your claims. Even if you know all this to be true, a reader may not, and that reader may not be trained to know what is true/not. We're about teaching people on Bio.SE, so by providing links to useful and supportive materials, you're helping out those that read the question a lot more. [Reputable] Support also helps other users feel more confident in your answer, which often leads to more upvotes (e.g., see here). Thanks!


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How to determine if twins are identical or fraternal if only one is alive?
I had a twin brother who died at birth. I've missed him all my life, and have been curious to know if we were identical or fraternal.
Is there a test to determine whether we were identical or fraternal?

This can often be determined by ultrasound during pregnancy, so your parents may know. Are you also male? Is the body still accessible?

@canadianer I was born in a country where technology such as ultrasound was not available, so my parents don't know. Yes, I am male. No, the body is not available as he died thirty years ago.

It seems to me that the answer would be no, then.


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How quickly do bacteria lose genes after selection has been removed?
If bacteria are subject to a biocide and then that biocide is removed from the population, how quickly will they lose that gene that encodes for resistance?


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How complete is the information in DNA?
Everyone talks about how DNA is the "molecule of life" and "the set of instructions for building you." How complete are the instructions, really, though? To make the question concrete, say I were to remove all of the DNA from a bacterium and replace it with the nuclear DNA from a eukaryote, would the cell (and it's daughters) be able to transition into the same sort of eukaryote as the DNA source? Granted, the lack of mitochondria would be a huge hindrance, but assume we could add some when the bacteria swelled up to a large enough size to accomodate them inside of it. Are there other barriers to this process?
I know that adding any single gene for producing a protein would function as expected when added to a bacterium, but would the lack of a nucleus and organelles prove fatal, or does the nuclear DNA have the information needed to build them up using only the machinery available in a bacterium?
What about an archaea? Or going the other direction - remove the nucleus from a eukaryote, add bacterial DNA, does the cell and its daughters survive to become bacteria?

If you want an analogy, it would be like having a hard drive containing all the specifications for all of the hardware and software necessary to read the information on the drive, as well as the manufacturing instructions for all of the machinery need to manufacture the computer, to manufacture the machinery needed to manufacture the machinery to manufacture the computer, and down the line to extraction of raw resources. The information is 100% complete, and totally sufficient to build a second set of all the machinery, but can't do it if you are just holding the bare drive.

Barrier? Yes Prokaryotic and eukaryotic cells differ in DNA replication.
So a prokaryotic cell would never replicate to form a eukaryotic cell. As of Mitochondria, Mitochondria have their own DNA and would replicate normally. I am not so sure about swapping with Archae though

@Soura Not to mention, bacterial DNA is partially methylated. Replacing bacterial DNA with the DNA from some eukaryote would not even if only for the reason that bacterial replication machinery requires this methylation.

This is a good question, because the answer to the overall question (is the information in DNA complete - yes) is not the same as the one to the more specific ones (would a cell survive if the DNA was swapped with that of another life form - no). Let me elaborate:
The information in the DNA of in any given organisms (except for a virus) IS complete. This means that the DNA has 'code' for all the molecules required to build and sustain this organism.
However, the DNA of an organism alone (or placed inside an unnatural environment like a completely different cell) is not sufficient to actually make or build that organism. The reason for this is that, while the DNA has all the necessary code, without the correct machinery to actually read that code nothing can or will happen. Eukaryotes and bacteria are so vastly different (which is to be expected after millions of years of evolution for both), basically all the different machineries are not compatible anymore: transcription binding sites are different, gene structure (exons/introns vs. operons) is different, Ribosomes are different, ... [btw this also means that just putting the gene of an eukaryote into a bacterium doesn't work, researchers have to modify it accordingly to work].
Even between different eukaryotes (and probably some bacteria but I'm not sure about that) exchanging the nuclear DNA would not produce viable cells (or at least not ones that could grow into an organism), since again the transcription machinery would not match up sufficiently.

"[btw this also means that just putting the gene of an eukaryote into a bacterium doesn't work, researchers have to modify it accordingly to work]" Thanks, in particular, for clearing up that misconception of mine. Is it a difference in the codon to peptide mapping, or maybe something in how the dynamics of folding work?

@SeanLake The main problem is the difference in gene structure (bacteria don't have introns). Codon usage (the frequencies of individual codons, not their meaning) can make problems, but will not prevent expression. Folding problems can also exist, but you can still make pretty much eukaryote protein in bacteria - just not necessarily always functional/correctly folded.


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How hard it is to determine a 3d structure of a protein?
I seeing tens of thousands of PDB files on the internet. I really want to determine a 3D structure of my protein of interest. I've heard that 3D structure determination is a complex, expensive, and specialized procedure that can take months or years and is hard to perform routinely or even purchase commercially.
Could you please explain why and how hard it is? What are the requirements and how big of a budget is typically needed to perform this kind of experiment?

It really depends on the protein. Which protein are you interested in? Or if you want to keep that secret at least tell us what type of protein it is... is it an integral membrane protein, or is it membrane associated? If yes then your experiment will be hard, but not necesarily impossible. If you want to discuss it of thread, send me a mail at (jan@mbg.au.dk) and I will try to help you. I am a trained structural biologist with significant experience in protein crystallography.

From personal experience, if your protein is not membrane associated and is generally stable in solution, it will usually take ~5-10mg to find possible crystallization conditions. I recommend starting with commercial screens and optimizing from them. Be aware that you may observe crystals that are not protein crystals in certain conditions. If you want help send me an email at the email in my first comment.

@JeppeNielsen Hi Jeppe ! Thank you for your enthusiastic and kind response. In near future, I'm planning to design a protein (currently non-membrane protein) and just want to see the final 3d structure result of it, I will contact you later if i need help from you. Thank you very much!

One warning before going heads in is that crystallography is of course only possible if the protein is capable of crystalizing. If you want to know more about biomolecular crystallography, read the book with the title biomolecular crystallography by Bernhard Rupp, it is more or less the goto source for all protein crystallographers.

@JeppeNielsen Thank you very muchhh! I will read that book. You're so kind!

I can attest from experience, the answer is "very"!

Experimental protein structure determination is hard: the most common method is X-ray crystallography, which can be done in a few months if you are lucky and can take years if you're not. The problem with X-ray crystallography is that you need good protein crystals, and in most cases, proteins don't crystallize very well, so it takes a lot of time (and a lot of purified protein) to get the right crystal. (In the comments section Cody added some good links with more in-depth abut X-ray crystallography for structure determination relating to ATP synthase).
The cost is mainly based on the materials & manpower you need for this, and you need to test a lot of different solutions to crystallize your protein in, which aren't very cheap. If you don't have access to specialised equipment for making the crystals (mostly pipetting robots) or the measurement (X-ray beamline), this is going to be super expensive.
Crystallography requires protein crystals, which are sometimes too troublesome to obtain. Other methods that do not require crystals, such as NMR and cryoEM, are even more difficult to perform though less luck dependent. These techniques rely on very expensive equipment and often cannot resolve the structure as precisely as protein crystallography. So unless you can find one of the few people who have experience with these methods, you'll run into a lot of additional problems.
There is also computational structure prediction, which only needs a powerful computer. However, unless your protein is very similar to one with a known structure it will probably not work reliably. As mentioned in the comments there are web server's for the established methods and progress is constantly made on new(er) algorithms, so depending on your needs it's definitely worth a shot to try computational structure prediction.

For what it's worth, there are many web servers for homology modelling, so all you need for that is a protein sequence and a browser.

Note that computational predictability recently made a giant leap forward and seems to work quite well (requiring primarily DNA sequences of many species rather than similarity to known protein stucture or computational folding simulations) http://science.sciencemag.org/content/355/6322/294

Two interesting & relevant papers showing how X-ray crystallography is used to determine protein structure are: Structure of ATP synthase from Paracoccus denitrificans determined by X-ray crystallography
at 4.0 Å resolution, and a review, The ATP synthase: the understood, the uncertain and the unknown. What's particularly nice about these is they deal with a protein complex virtually everyone is familiar with, yet has been very challenging to characterize using our standard techniques.

In fact, computer approach is so hard (this is a combinatorial problem where exploring all the possibilities is not feasible), that some scientists have designed Fold It!, a game where players must find the best protein folding. There is a field of work where scientists look at best player's strategies to design their own heuristics.

I'll address NMR for structure determination. It is the less common method, only ~10% of protein structures are determined this way, though it has e.g. advantages for nucleic acids and more than a third of those was solved by NMR. Take any numbers here as very rough estimates, there are a lot of factors that influence the difficulty and cost.
For NMR, the single most important factor is size. A stable, well-behaved protein of 10-20 kD is pretty much routine. Large proteins are either very difficult to measure or outright impossible by NMR.
You need large quantities of protein for X-ray and NMR, but in the case of NMR you also need it isotope-labeled. Uniformly labelling proteins 15N/13C isn't all that expensive if you can express your protein in E. coli in minimal medium (around $100 per liter medium or so, mostly in 13C glucose), but it can get really expensive very fast if you need full medium or anything fancy.
Your protein needs to be stable in solution for a few days at least, a single 3D experiment can take multiple days to measure. If your protein is barely stable enough, you also have to produce much more protein because you need to use many samples to perform all necessary experiments. A complication here is that you can't add a lot of salt to an NMR sample without drastically reducing the sensitivity of the NMR experiments. But some proteins are hard to get stable in a low-salt environment.
You need something like a few weeks of measurement time on a high-field NMR spectrometer, though this depends a lot on the size of the protein and the concentration you can achieve in your sample and the general difficulty of assigning the protein resonances. This kind of spectrometer can cost a few millions, and you need to supply liquid nitrogen and liquid helium to keep them working. Something like a $1000 per day measurement time is a number I've heard about the cost, but there are a lot of factors that go into this and I can't say how accurate this number is.
Then you need to assign the resonances in your protein, which takes a single person several months. This again varies a lot depending on the difficulty.
Then you need to calculate the structure, and typically this requires several rounds of refining the assignment and analysis and redoing the calculations. It's not really expensive in terms of computer power, but it takes quite some work by the person running the calculations and checking them.

a 2007 article says "The largest monomeric protein structure solved by NMR to date is that of malate synthase G (MSG), an 81.4 kDa enzyme " https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596980/

@DavePhD The fine print is important here, they solved the global fold of the protein, that's not a full structure. And even for that they had to pull out quite a few tricks with specific labeling and deuteration. If you're not Lewis Kay, trying to solve the structure of such large proteins by NMR is probably not a good idea.


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A compound was proposed by error but then showed very good inhibitory properties. How to argue this in a manuscript?
In a project, we performed some virtual screening calculations in order to predict inhibitors, and then purchased the compounds and tested them in the lab. One of them was a very good TK inhibitor (IC50 nM).
However, when we processed the results we realized that the presence of this particular compound in the original list of virtual screening hits was due to errors in the original calculations (it was added to the list by random factors, not by docking score).
So now we are writing the paper and we wonder how to argue this. We can not just tell the story like in this post (it was discovered by randomness or by our error). How would you argue this?

It was in your negative control set and it worked. I have had a lot of random mutations in my library designs which I did not plan on end up working. You just say it in the results section and don't try and matriculate on it too long. That is only possible if you have real molecules from the docking data that also worked. If that is so, you can definitely add this as a fluke and no one will argue. However, if it is the sole result and conclusion, it may be much harder to spin a high impact manuscript.

I'm voting to close this question as off-topic because it is about the process of submission of papers to journals and not about biology itself. Any answer is also subjective.

@David yes, [academia.se] might be a better home for this. On the other hand, an understanding of the basic biological concepts involved is helpful for answering. I think it could go both ways.

Be honest (and possibly split the papers).
If the compound was identified as an error and you want to include in a paper describing the process of your simulation and the effectiveness of the predicted inhibitors, you'd have to do so as a sort of negative control for your calculations (unless there is some way to reproduce/rationalise why it showed up randomly). Since this is the only good inhibitor you have, you'd have to conclude that your calculation isn't much better than chance, or explain why it is better even though you found a better inhibitor by chance. If you have reason to argument that your calculations are good and make sense then exclude the 'random' inhibitor from that paper. You can the write an individual paper about a good inhibitor, the fact that you found it by chance isn't that important anymore.


text:
Why does it hurt the next day after doing significant exercise?
I think this is a fairly common observation that if one does some significant amount of exercise, he/she may feel alright for the rest of the day, but it  generally hurts bad the next day. Why is this the case?
I would expect that if the muscles have undergone significant strain (say I started pushups/plank today), then it should cause pain while doing the strenuous activity, or during rest of the day, but it happens often that we don't feel the pain while doing the activity or even on that day, but surely and sorely feel it the next day.
Another example - say after a long time, you played a long game of basketball/baseball/cricket. You generally don't feel any pain during the game/that day, but there is a good chance it will hurt bad the next day.
I am trying to understand both - why does the pain not happen on that day, and why it does, the next day (or the day after that).

I like your question. I've experienced, though, that sometimes this pain is the second day after, instead of next day. Might depend on the nature of the exercise.

@DonBranson interesting point. I have added that in my question now

It should be noted that one warning sign of actual muscle damage, regardless of the mechanism, is "myoglobinuria", the presence of a rust-colored sediment in the urine.  If you experience this (other than perhaps on rare occasions when you know you've "overdone" it) then you should have a neurologist (yep, a neurologist) investigate.

@HotLicks, interesting. Why neurologist?

@user1993 - Neurologists are trained in muscle disorders.

Unlike the conventional wisdom, the pain you feel the next day (after a strenuous exercise) has nothing to do with lactic acid.
Actually, lactic acid is rapidly removed from the muscle cell and converted to other substances in the liver (see Cori cycle). If you start to feel your muscles "burning" during exercise (due to lactic acid), you just need to rest for some seconds, and the "burning" sensation disappears.
According to Scientific American:

Contrary to popular opinion, lactate or, as it is often called, lactic acid buildup is not responsible for the muscle soreness felt in the days following strenuous exercise. Rather, the production of lactate and other metabolites during extreme exertion results in the burning sensation often felt in active muscles. Researchers who have examined lactate levels right after exercise found little correlation with the level of muscle soreness felt a few days later. (emphasis mine)

So if it's not lactic acid, what is the cause of the pain?
What you're feeling in the next day is called Delayed Onset Muscle Soreness
 (DOMS).
DOMS is basically an inflammatory process (with accumulation of histamine and prostaglandins), due to microtrauma or micro ruptures in the muscle fibers. The soreness can last from some hours to a couple of days or more, depending on the severity of the trauma (see below).
According to the "damage hypothesis" (also known as "micro tear model"), microruptures are necessary for hypertrophy (if you are working out seeking hypertrophy), and that explains why lifting very little weight doesn't promote hypertrophy.
However, this same microtrauma promotes an inflammatory reaction (Tiidus, 2008). This inflammation can take some time to develop (that's why you normally feel the soreness the next day) and, like a regular inflammation, has as signs pain, edema and heat.
This figure from McArdle (2010) shows the proposed sequence for DOMS:

Figure: proposed sequence for delayed-onset muscle soreness. Source:
 McArdle (2010).
As anyone who works out at the gym knows, deciding how much weight to add to the barbell can be complicated: too little weight promotes no microtrauma, and you won't have any hypertrophy. Too much weight leads to too much microtraumata, and you'll have trouble to get out of the bed the next day.
EDIT: This comment asks if there is evidence of the "micro tear model" or "damage model" (also EIMD, or Exercise-induced muscle damage). First, that's precisely why I was careful when I used the term hypothesis. Second, despite the matter not being settled, there is indeed evidence supporting EIMD. This meta-analysis (Schoenfeld, 2012) says:

There is a sound theoretical rationale supporting a potential role for EIMD in the hypertrophic response. Although it appears that muscle growth can occur in the relative absence of muscle damage, potential mechanisms exist whereby EIMD may enhance the accretion of muscle proteins including the release of inflammatory agents, activation of satellite cells, and upregulation of IGF-1 system, or at least set in motion the signaling pathways that lead to hypertrophy.

The same paper, however, discuss the problems of EIMD and a few alternative hypotheses (some of them not mutually exclusive, though).
Sources:

Tiidus, P. (2008). Skeletal muscle damage and repair. Champaign: Human Kinetics.
McArdle, W., Katch, F. and Katch, V. (2010). Exercise physiology. Baltimore: Wolters Kluwer Health/Lippincott Williams & Wilkins.
Roth, S. (2017). Why Does Lactic Acid Build Up in Muscles? And Why Does It Cause Soreness?. [online] Scientific American. Available at: https://www.scientificamerican.com/article/why-does-lactic-acid-buil/ [Accessed 22 Jun. 2017].
Schoenfeld, B. (2012). Does Exercise-Induced Muscle Damage Play a Role in Skeletal Muscle Hypertrophy?. Journal of Strength and Conditioning Research, 26(5), pp.1441-1453.

is microtrauma an event at the cellular level?

Out of personal interest, do you think that inflammatory reaction could also cause general tiredness/exhaustion? I have heard of multiple people (including myself) that while they do sleep well after exercising and the exercise does increase their overall energy level compared to a more sedentary lifestyle, they are very tired the next day.

so is it like wear and tear of the cell, then? And if so, then what is the actual cause of the delay in pain perception?

@user1993 First, it's not like all the cells have membrane damage: it depends on the intensity of the exercise. Second, as any inflammatory process, it takes some time to develop, specially if the damage is small and diffuse. There is no delay in pain perception: the delay is related to the ability of the inflammatory process to promote pain. It's not instantaneous.

@skymningen Inflammation does changes histamine (which is a neurotramsitter), prostaglandin, bradykinin etc levels in the blood. However, there are so many other substances and processes involved that I think it's complicated associating that next-day fatigue/tiredness to the substances released by inflammation, or to the inflammation itself at cellular level.

@user1993 It's not unique to exercise. Most kinds of internal damage take some time to manifest fully (e.g. burns, radiation sickness...). Cells require constant maintenance - they need to continually replenish all sorts of damaged machinery. When you do enough damage, they can't replace the damaged parts fast enough, and the cell gets automatically destroyed. If enough cells get destroyed, you get an inflammation, which can be quite painful. With enough damage, you get more vulnerable to disease. The reconstruction of course takes a lot of the body's resources, causing tiredness and hunger.

Has the damage hypothesis model every validated scientifically?  For example, has there ever been an experiment that quantified micro-tears in muscle before and after strenuous exercise?  Has anyone ever seen a micro-tear?

But why is the DOMS so bad when you start with a new exercise? Your example with the barbell is actually contrary to my (and others) experience: When you are used to an exercise you can do it as hard and often as you like, you’ll only have tired/“heavy” arms/legs the next day, not DOMS. A beginner can get severe DOMS from exercise which doesn’t even feel hard or exhausting.

Try to put twice the weight (don't do that!) and do the same reps. You'll have a severe inflammation, or even worse, a rupture or a fracture. Besides that, the "heavy" arm is actually a moderate DOMS. Regarding the new exercise, your muscles don't have the necessary strength to perform that new "movement".

It should be noted that in some people (somewhere between 1% and 3% of the population, depending on who's counting) there is another mechanism for delayed muscle pain.  Myoadenylate Deaminase Deficiency (MADD) is a genetic condition whose primary symptom is pain and cramping with an onset about 36 hours after moderately intense exercise.  The pain often persists (due to muscle damage), resulting in a "pulled muscle" sensation which lasts for weeks or months.
The condition is caused by a genetic defect which causes the AMP<=>ATP recycling mechanism in the muscles to "leak" AMP into the bloodstream, weakening the muscles' ability to continue exercise.
Significant relief of symptoms is often achieved by taking D-ribose orally.
And another somewhat rarer genetic disorder which can result in muscle pain is McArdle's Disease.


text:
What is the difference between scale vs cataphyll?
What is the difference between scale and cataphyll in botany - aren't these the same type of organ?
E.g. do cycad cones have scales or cataphylls? Pine cones have scales, I understand the compound nature of pine cones - does that make them scales?
On fern petioles/stipes there are often scale-like organs I've seen called scales (though they are not very scale-like).

Welcome to Biology.SE! What research have you done before asking it here?

According to "Plant Identification Terminology: An Illustrated Glossary" (Harris & Harris, 2001):
Scale:

Any thin, flat, scarious structure

Note: "Scarious" = Thin, dry, and membranous in texture; not green

Cataphyll:

Brown or colorless scale-like structures believed to be modified leaves

So "scale" is going to be used more broadly, while a "cataphyll" (though scale-like) is more specifically always some type of modified leaf.
According to Wikipedia:

Cataphylls include bracts, bracteoles, and bud scales, as well as any small leaves that resemble scales, which are known as scale leaves.

You can find good illustrations of cataphyll examples here.

Thanks, I understand cataphylls a bit better. With scales, how does this definition fit in with scales on conifer cones? And do cycad cones have scales or are they just called sporophylls? I see in "Pterophytes and Gymnosperms" (Kramer and Green, 1990) they say cycads have 'scale-like sporophylls'. Why are they scale-like and not just scales?

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


text:
Do artificial light sources cause enough fatalities in light-attracted insect species to cause eventual extinction?
There are various theories about how insects are drawn to light bulbs because of navigation mechanisms based on the sun and moon's position in the sky. It makes sense for that to work when the only major light source on Earth was high in the sky at a very slowly changing angle, but now that we have artificial lights it seems like that would severely interfere with the regular life cycle of insects. Being stuck buzzing around a light bulb for almost half of every day seems like it could be damaging to the life expectancy of each bug, and therefore damaging to the species as a whole.
But the reality is, most of the "livable" surface on Earth is not covered in cities, so most of the bugs aren't affected by these artificial lights.
So that leaves me wondering, if we expanded our cities to cover most of the earth livable surface, would we potentially kill off a large portion of the bugs on earth that are drawn to light or rely on bugs drawn to light as a food source?
That's sort of a hard question to answer though, because of so many factors, however I think the root of the question is a simpler one:
Do artificial light sources cause enough fatalities in light-attracted species to prevent them from successfully reproducing at the necessary rate for survival? (assuming the whole species were subjected to such light sources)

Short answer:
Yes, it is highly likely that artificial light sources may cause such high mortality that insects become (locally) extinct.
Long answer:
As you will understand, it is almost impossible to perform an experiment where lights cause extinction of a species. However, we have a lot of 'circumstantial evidence'; cases where it is clear that lights have dramatically decreased species richness (which means local extinction). If lights can cause local extinction, they can also cause global extinction if, as in your question, their entire population would be exposed to light.
Percentage of insects attracted/killed by light
Why insects are attracted to light remains unanswered, but that they do is clear. Also, it is known that insects that are attracted suffer an increased mortality, due to the light itself and due to predators actively hunting the blinded and inactive insects. The reported estimates of the number of insects that are attracted and killed by a light source differ and depend on the light source (color mainly), the background lighting (moon!) and other factors. A fair estimate is that about a third of the insects that are attracted by a light source are killed
A third is a very high mortality, that is off course added onto the other (natural and man-made) mortality insects suffer from. It is very likely that this would cause insect populations to become extinct, especially those already at risk.
Based on observations
Eisenbeis&Hänel give a number of examples that show that insects populations dramatically decline when exposed to lights:
- the number of insects drawn to the lights of newly build fuel stations is high in the first years, than rapidly declines.
- the butterfly fauna in remote Austrian valleys declines after introduction of lighting (for tourism).
- The number of caddisflies drawn to lights exceeds that of the number found in a stream.

Nice answer. Note that it's a third of the insects attracted to a particular bright light source that are killed estimated from that paper, not a third of all insects.

@Bryan. Good observation. I've edited that in.


text:
Can anyone identify this locust / grasshopper in Florida, USA?
Found in Pinellas County, Florida

Can you add some more details about it, including some more images?

Two more images added. What other details would you like?

@Stewart, for future reference, see the guide for writing species ID questions -- it'll tell you what info is typically needed. Thanks.

It appears to be Romalea microptera, or the eastern lubber grasshoper, which is commonly found in the southeastern United States, including Florida.
https://en.wikipedia.org/wiki/Romalea_microptera
http://eol.org/pages/965190/overview

Photo by Steve Smith.

Eastern lubber , although they get to TX. Kill it , if you have any bulb type flowers . They will eat all amaryllis leaves and the whole bulb. The immature are gloss black with red pinstripes ; so pretty I made the mistake of not killing them one year.


text:
Variance of Stochastic Growth Rate for Average Population Size Over Time
I'm interested in calculating the variance of the stochastic growth rate for the average population size over time,
$$\ln \beta = \lim_{t\to\infty}\dfrac{1}{t}\ln V[N(t)]$$
which shows that the variance of $N(t)$ grows at a rate $\beta$.  The equation to compute this is given in the book "Matrix Population Models" by Hal Caswell.  The variance can be calculated as,
$$\beta = \lambda_1^{(\bf{B}_2)}$$
where $\lambda_1$ is the dominant eigenvalue,
$$
\begin{align*}
\bf{B_2} &= \bf{F_2}[\bf{P}\otimes(\bf{I}\otimes\bf{I})]\mathrm{,} \\[1em]
\bf{F}_2 &= \mathrm{diag}({\bf A_1 \otimes A_1, \ldots, A_k \otimes A_k})\mathrm{,}
\end{align*}
$$
$\bf A$ are the population projection matrices of dimension $s$ from $k$ independent environments, $\bf P$ is the column-stochastic transition matrix of dimension $k$, and $\bf I$ is the identity matrix of dimension $s$.  I tried doing this in R using the goldenheather (Hudsonia) example from the Caswell book that can be loaded into R as follows,
library(popbio); library(Matrix); data(hudsonia)

I ended up with a value for $\beta$ of 0.9366351.  This cannot be right, the variance is way too high.  I must be doing it wrong, or perhaps there is a mistake in one of the equations (very, very likely the former).
Here's my code (if it helps),
s = NROW(hudsonia[[1]])
k = length(hudsonia)
P = Matrix(1 / k, k, k)
I = Diagonal(s, 1)
F2 = bdiag(lapply(hudsonia, function(i) kronecker(i, i)))
I2 = kronecker(I, I)
P2 = kronecker(P, I2)
B2 = F2 %*% P2
lambda(B2)


text:
Why do birds flap/shake their wings?
Here is a video that will show the behaviour I'm interested (see between 12:30 and 12:32).
I want to know if this behaviour has a name and why birds are doing this. I observed this many times, with offsprings getting fed, females and males adults. I'm curious about studies that looked at that behaviour.

I'm not enough of an ornithologist to answer this, but I'm pretty sure this is a begging behaviour. Using that term should get you somewhere searching for studies. The 2 seconds in your video isn't the most clear example, but here is more: https://www.youtube.com/watch?v=dhNOLL6CZog


text:
Phylogenetic Independent Contrasts with discrete traits
I understand that PICs are normally only used for continuous traits. However, on this how-to site (https://www.r-phylo.org/wiki/HowTo/Phylogenetic_Independent_Contrasts) there is mention of "Discrete traits can be coded as continuous variables (see ?contr.treatment) and analysed as usual, if they are independent (explanatory) variables."
However, I'm having trouble understanding the commands described in ?contr.treatment and how they relate at all to using discrete traits in PICs. I assume it is a way to transform discrete into continuous data (or at least the appearance of cont. data) so as to perform the PIC, but I don't know how to get there from that hint.
This would very much help analyze my data, which includes both continuous and discrete data. I've already performed a phylogenetic logistic regression, but I feel that PICs could help cement my case if possible to perform.

Assuming that by "discrete", you mean "discrete and ordinal" (like 2, 21, 7, 12) and not "discrete and nominal" (like red, blue, yellow, green), then it is really easy. It just mean you can just use your numbers. The contrast between lineage with average trait 6 and lineage with average trait 9, the contrast is therefore 3.
If your data are nominal, then there is no way to calculate a contrast.
Not however, that typically you might violate assumptions of the PIC model. Make sure to know those assumptions and have a feel of whether you seem to respect them.


text:
When does a jalapeño begin to produce heat/capsaicin?
I have a small Jalapeno plant in my apartment. About two weeks ago, it started producing a few flowers. In the last few days, many of them have started to turn into fruit; however, a few of the flowers have fallen off. The flowers do contain some seeds. They look rather like this:

Note this is not a picture of my plant (my flowers are white) but apart from the color it looks quite similar.
I tried munching on the seeds to see if they were hot. They weren't at all. I believe it is a common misconception that the seeds are where capsaicin concentrates, but should there have been any heat? Is there none in the seeds at all? Or was it too early in development?
Related questions: Do you think these seeds were viable at this point, or would they need to develop in an actual pepper fruit?

The reason the 'seeds' you ate weren't hot is because they're not seeds. What you thought are the seeds in the pepper flower are its anthers. The anthers are the pollen bearing parts of a flower. The unfertilized, and therefore undeveloped, seeds would be found in the flower's ovary which is at the base of the petals. The parts of a flower are labeled in this diagram.

I've tried both the seeds and the flesh of jalapeño peppers and noted the 'heat' in both but personally, I found the seeds a little hotter.


text:
Where in the nervous system are synapses chemical, and where are they electrical?
Paraphrased from the Wikipedia article "Synapse":
There are two fundamentally different kinds of synapses:

Chemical synapses, which convert electrical activity in the presynaptic neuron into the release of neurotransmitters via the activation of voltage-gated calcium channels. The released neurotransmitters, which vary in type by cell, bind to receptors of the postsynaptic cell, giving rise to complex behaviors.
Electrical synapses, in which presynaptic and postsynaptic are connected by "gap junctions" or synaptic clefts capable of passing electrical current, resulting in rapid signal transduction.

Are there certain structures and locations in the nervous system that are mostly or exclusively chemical synapses, and certain ones that are mostly or exclusively electrical? Or, are they mixed throughout the nervous system?
For example, one might suppose that the neurons which transmit signals from brain to limbs might be electrical, due to the apparent advantage of fast transduction times in this scenario. On the other hand, it might be advantageous for the brain to be capable of more the dynamic, albeit slower, signal transmissions made possible by chemical synapses. Are these intuitions accurate?

Synapses are almost all chemical, the electrical synapses are more of a "special case".
The speed of transmission across limbs, etc, has very little to do with the speed of the actual synapse. The signal itself is conducted electrically inside a given cell (this is an "action potential"), aided in many cases by insulating myelination. The synapse is just the endpoint.
Some places where electrical synapses/gap junctions are present are:

Between cardiomyocytes, to synchronize heart contraction
Between certain networks of inhibitory interneurons in the CNS
In some (but not nearly all) reflex circuits


text:
How outdoor/wild plants survive without any proper human support?
I will take care of indoor plants because it was growing in my lawn
if I don't care then parasitic vines will destroy my plants.
But how plants take care of itself which are still surviving in forest without any human support?

Welcome to Biology.SE! What research have you done before asking it here?


text:
Why do hand/fore-arm muscles "lock up" after very high-powered effort?
Inspired from Why does it hurt the next day after doing significant exercise? with its excellent answer:
In climbing, you can put tremendous load on the hand/fore-arm muscles (specifically, flexor pollicus longus and flexor digitorum profundus). What happens is often that you are not just fatigued, but that the muscles seem to "lock up" - they subjectively feel "hard", it seems impossible to relax and the problem does not go away after a few minutes, by stretching (which will actually become quite painful) or by self-massage.
The muscles are not necessarily showing the burning sensation that indicates lactate buildup according to the answer for the linked question. This effect seems to be a main cause for athletes to prematurely end a training session because there's little hope to solve it except for a long (hours...) rest. People have trouble opening doors etc. because the muscles seem to be completely wasted. Onset is immediate during or after a straining exercise, not later, like DOMS would be. After a good nights sleep, the problem usually seems to go away, it is not a day-long soreness.
Is that effect rather related to damage (micro tears etc.) or some chemical process? Is there a good way to prevent it, either in the short or long term, i.e. by training specifically for/against it? Are you aware of other muscles that show the same behaviour? I have only experienced it in those.


text:
Why don't antiseptic agents kill 100% germs?
I've seen innumerable antiseptic, mouthwash, handwash advertisements that claim to be able to eliminate as much as 99.9% of all germs over a surface...but why not the remaining 0.1% (i.e- why can't they eliminate all germs)?

Clarifications:
What they mean by "germs":
Being a student of Biology, I can tell that the term "germs" is crudely defined. I would prefer to use "pathogens" (less ambiguous), and I suppose the guys that market these products have (roughly) the same idea in mind. Pathogens normally include bacteria (monerans), protozoans, fungi and viruses... so I guess these are the "germs" they're talking about.
What I'm looking for in an answer:
Why is it that these (commercial) products can't eliminate 100% of all pathogens? Is this due to the inability of antiseptics to act on a particular (class of) organisms? If so, what's the problem there? Or is it because, the guys who market stuff like this assume an arbitrary amount (0.1%) of the pathogens present on a surface (say, the human hand) is located in microscopic niches that are inaccessible to the antiseptic solution? (If it isn't possible to provide a blanket statement in this regard, use of Listerine as an example will suffice)
In other words:
Is an antiseptic's inability to eliminate 100% of all germs due to its "chemistry", or is it due to physical factors?
Also,
Do antiseptics/mouthwashes/handwashes even kill 99.9% of all germs in the first place? Or is it (as I strongly suspect) an example of marketing fraud?

I think they leave that 0.1% just so that they can pull their hands away in case of any infections. But your question is too broad, in the sense that you are asking too many qiestions at the same time. You need to narrow it down.

It's amazing that, for the layman (blame media on that), 99.9, 99.95, 99.992 or 99.9999435 are all the same thing. "99.9" is not a number anymore, it's just an idiomatic expression, meaning "almost all".

@gerardo why don't you add another answer explaining that part? You'll definitely get upvotes, and it might bring this into hot questions list ;)

In a first year lab I used to teach, the students would determine the zone of inhibition for different antiseptics in an agar diffusion test. Listerine didn't kill anything.

I suspect that 99.9% has more to do with marketing and lawyers than biology. They don't promise to kill all the germs so they can't be sued when they don't. On the other hand, it sounds like a promise to anybody who believes in the 3 second rule.

Microbes vary greatly in their ability to survive a particular method of sanitizing. For instance, giardia cysts (a protozoan) are hard to kill with halogens because they have a hard shell. Clostridium botulinum spores in food can survive cooking at 100 C and still cause botulism afterward.

@mmesser314 -  for non-native English speakers: 3 seconds rule means you can safely eat food dropped on the floor if you pick it in 3 seconds or less. Of course not based on any science.

@petermasiar I thought it is 5 second rule coz thats what I've heard everywhere? Has it been modified? I recently also saw many news reports saying "science proves 5 second rule is true" (didn't read any of them though)

@another'Homosapien' - I am not sure who would finance such research, and why. Urban dictionary in my link does not pretend to be scientific, but is (IMNSHO) great resource for non-native speakers to decode expressions obvious for native speakers, but puzzling for others.

I also found 5 seconds rule which says exactly what 3 seconds rule says. And both are correct! Amazing thing, this science!

@another'Homosapien' I just posted it.

This is actually an interesting question! Let me answer both the parts separately, taking the example of Listerine® mouthwash.

Is an antiseptic's inability to eliminate 100% of all germs due to its "chemistry", or is it due to physical factors?

In most of the cases, this is due to the physical factors. Clearly, your mouth is not a flat surface. It has many depressions and elevations. And these irregularities are the perfect hotels for all kinds of pathogens. Also, it is difficult for most chemicals to reach those spots and stay there for long enough so that they can act on the pathogens. Thus, most of these chemicals would be unable to kill 100% pathogens because of their inability to reach all of them. Also, in rare cases, it might also be due to chemical factors(!) Yes, I'm talking about antibiotic resistance. And in that case, it would be practically impossible to kill 100% pathogens, no matter whether they're hidden or exposed.

Do antiseptics/mouthwashes/handwashes even kill 99.9% of all germs in the first place? Or is it (as I strongly suspect) an example of marketing fraud?

For that, lets first see what Listerine® contains. As given on its website, its main ingredients are (I'm simply copying what they write on their page, followed by checking whether its true):

Eucalyptol – with antibacterial properties, this eucalyptus-derived essential oil works as an anti-fungal agent within the mouth.
Methol – this natural oil as germ-killing abilities to help halt the growth of bacteria.
Thymol – this powerful oil is derived from the ajowan herb, and helps decrease the risk of gum disease.
Methyl Salicylate – for minty freshness from morning til night, the flavouring agent in this essential oil is, well… essential!

We just need to know whether these ingredients really work or not (why? We'll talk about this later on) and I'll skip methyl salicylate for this (they don't even claim that it is antimicrobial). Beginning with eucalyptol, it has been shown that oil of Eucalyptus globulus (of which eucalyptol is a component) has antimicrobial properties against Escherichia coli and Staphylococcus aureus (see Bachir et al, 2012). It has also been shown to possess antifungal properties (Safaei-Ghomi et al, 2010). Coming to methol, it has also been shown to have antibacterial properties against various Staphylococcus and Lactobacillus species (Freires et al, 2015). Finally, there have been lots of studies about the antimicrobial properties of thymol. You can check out the Wikipedia page for information.
So, where is the percentage? The point is, the exact percentage depends on a lot of factors. When an enterprise, such as Listerine®, claims that their product has been shown to be 99.9% (or any number) efficient against bacteria, they need to cite the particular study through which they claim this number. But they can not, in any case, be definite that their product will be 99.9% effective everytime. How effective a product is also depends on the conditions under which it is tested. Mostly, these tests are performed on a petri dish in a laboratory, something very different from your mouth. Thus, although they can claim that their product is scientifically proven to be 99.9% effective, they cannot claim it to be 99.9% effective when you use it. Again, they cannot claim 100% effectiveness because this makes them liable (saying our product has been shown to be 100% effective requires them to show that even a single microbe did not survive on the petri dish they used for experiment). Also, this gives them a way to escape in case anybody complaints about their product not being effective (since they caught infection even after using their product). In such situation, they can easily say that their product is not 100% efficient!

I really like this answer! As much as I want to "accept" this, I guess it would be wise to give the question a day for more answers to (hopefully) trickle in. Thanks again! ^_^

I'm more familiar with the science having to do with water purification, e.g., using iodine tablets when hiking, but I think some of the science is the same. If there's dirt in your water, then there will be bacteria inside the dirt particles that can't be reached by the sanitizing agent. Similarly, if there's a speck of food caught between your teeth, listerine may be unable to reach the bacteria inside the speck of food. Pasteurization is much more effective at killing almost all organisms, because the temperature can't be sheltered against.

@bencrowell agreed, but you can't pasteurize your mouth :P talking about soaps, most of them just help you banish those microbes by flushing them with water (only antibacterial soaps do seem to "kill" them, albeit this is debated too)...

For Listerine, you are missing the main ingredient -- alcohol.  Depending on formulation, Listerine is about 22% to 26.9% alcohol.

Answers to this question point to this paper, which says "alcohols [are] significantly [less effective] at concentrations below 50% and is optimal in the 60 to 90% range". It also points out that alcohol is fungicidal, but not sporadical. As the question asks about "Antiseptic" and not specifically organic antibacterial/antibiotic agents, this seems very pertinent. I had another point I wanted some clarification on, but I can't remember it after brushing my teeth.

What does "99.9%" mean, anyway?
@another'Homosapien' already provided a nice answer, which explains the biological aspects of the question. However, following his/her advice, I'd like to talk about the mathematical aspect of the question. I'm a biology teacher only, but I always liked math and I have a deep respect for statistics and its branches.
We tend to generalize when thinking about big numbers, small numbers or approximations. That's normal and actually expected. We say that a given galaxy has 400 billion stars, or that the human body has 1014 cells. Those numbers are not exact, and no one expects them to be.
However, the problem with "99.9%" is different. That's not an approximation or an extrapolation for something that would be very hard or impossible to count, like the precise number of stars in M83 galaxy. That "99.9%" has become just an idiomatic expression.
99.76, 98.58, 99.98 and 99.92 are not the same number, They are close, but not the same. And, given the context, the difference can have a huge significance. Follow me:
Imagine that a given birth control pill A has a theoretical effectiveness of 99.96%, while a given birth control pill B has a theoretical effectiveness of 99.98%. They are both very high, so we will simply say "99.9%". However, the number of couples that get pregnant using the pill A is the double of the number of couples that get pregnant using the pill B (0.04% versus 0.02%).
I've heard several times that hormonal birth control methods have an effectiveness of 99.9%. That's just a generalisation. Let's see some real numbers (this data is from Hatcher, R. (2004). Contraceptive technology. New York: Ardent Media, Inc.) for some methods:

Progestin pill: 99.7% (it's not 99.9%)
Cooper T IUD: 99.4% (it's not 99.9%)
Depo-provera: 99.95% (it's not 99.9%)
Evra patch: 99.7% (it's not 99.9%)
Mirena: 99.9% (well...)

The examples abound. For instance, you can hear that DNA polimerase is accurate 99.9% of the time, or even 99.99%, if the speaker wants to transmit a higher precision. However, the real number is closer to 99.999999% (given an error rate of 10-8 per bp).
But nothing beats the TV ads for antiseptics and cleaning products. They all say "99.9%", and some of them say 99.99% (to make the message even more clear). However, these products don't kill "99.9%" of bacteria (be this either the number of cells or the number of species). The real number may be 98.46%, or 99.12%, or 99.98%... As @mmesser said in his/her comment, " that 99.9% has more to do with marketing and lawyers than biology".

"Huston, we have a winner": this brand not only added another "9" to the sequence, but also claims to be the fastest gun in the west.
Conclusion: in non-scientific media and TV ads in particular, "99.9%" is not a number anymore, it's just an idiomatic expression, meaning "almost all".

Well as a Microbiologist by trade, we use this numbers based  on log reductions on the forming units of the organism being tested. There is a limitation on the testing methods that cannot determine an absolute elimination of the pathogen.
For example, I perform the test and perform serial dilutions of the recovered organism and plate it on agar to be counted. Higher concentrations are hard and nearly impossible to count so we must use dilutions to achieve this and then multiply for the dilution factor to react an "exact number". So when I perform a 100 times dilution and the agar plate comes clean (no organism) growing the recorded number is not 0 but <100 because we cannot be sure about how many organisms should be there. I know this is a bit confusing but it is more like a safeguard to not give false information.

+1 Came here to say this - although the others make some interesting points and speculations about liability etc, this is actually the correct answer. Legally, a chemical must result in a 3-log reduction in titre during the specified contact time to be described as a disinfectant. (Source: I run a high containment pathogen lab and we use similar protocols to validate disinfectants whenever we add a new pathogen, want to test a new chemical, or want to modify our protocol - reduction in contact time, validation at low temperatures, etc.)

You could improve the answer by adding a labelled diagram of a serial dilution or some links, though.

I agree with answer of @another 'Homo sapien' - to 99.9% :-) but there is another angle on it:
From millions of bacteria present, few might be genetically different enough to be able to deal with whatever chemical mechanism it supposed to kill them (have resistance to it), and survive. Evolution at work.

Unlike you, I am just a computer programmer who had a pleasure to work for bioinformatics in academia for a decade. So I prefer to read explanations by experts, instead of pretending to be one. I am just a lurker here. Making my answer longer would add fluff, and I like concise answers.


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Detecting cancer in the hyperplasia phase using image processing and SEM
I was wondering if it possible or have someone tried before to use SEM or some other spectroscopy to detect an cancer evolvement in its hyperplasia phase:

It sounds like a good way to do it? I guess that's how biopsy works, but maybe there is a way to do test people in the risk groups using this method.

Your "SEM" link links to the same image you included below.

Not exactly spectroscopy, but microscopy is common for detecting pre-cancerous tissue as part of the standard Pap Test given to women at regular intervals throughout their life:
https://en.wikipedia.org/wiki/Pap_test
This is typically done by a team of cytologists (with pathologists confirming results, particularly in abnormal cases), but is beginning to have automated screening (with human oversight).
One of the problems with any form of screening is that the potentially problematic tissue needs to be observed, which is typically quite an invasive procedure. A potential melanoma is usually cut out prior to analysis, and I expect that any procedure involving a scanning electron microscope will also require tissue removal prior to analysis.
A more interesting development in the area of cancer screening is in looking for cell-free genomic DNA in blood; blood tests are much better tolerated for screening purposes in comparison to other tissue removal. With high-throughput short-read sequencing, it's possible for some cancers to see DNA changes before their effects are detectable through histological methods.
Here's a review paper on cfDNA screening, which is is generally negative about the whole thing:
http://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1002205
And one that is generally positive:
http://cancerres.aacrjournals.org/content/76/14_Supplement/LB-136.short


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Why is a butterfly actively looking for cool, dark spot, long before dark?
Here in Croatia, the Woodland grayling Hipparchia fagi flies constantly in the garden of my holiday home.
Yesterday, I observed that one of these bufferflies was actively looking for a cool/dark spot around 6 pm. First it hid at a wall in a shaded corner behind a bush. During the day these butterflies are very alert, but this specimen could be approached to a few cm. Finally it flew away, to take refuge inside the house, even more cool and dark. Again, it didn't move until I blew it away (couldn't lock it in, could I).
Now, my question is why this butterfly behaved like this.
I am convinced it did not seek shelter from the heat, because they keep flying during the hottest part of the day.
Was it already looking for a place to spend the night? That seems rather early. At 6 pm, the sun is going down a bit, but temperature is still around 30 degrees and it won't be dark for 3 or 4 hours. Other butterflies like Iphiclides podalirius are still active. Or has H. fagi a higher heat demand than other species? That seems inconsistent with its habitat (woodland). Any thoughts?


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Can elementary alternative splicing events be combined in more complex events?
I'm a computer scientist who is trying to understand alternative splicing. As the title says, I'm here to ask you if, from a biological point of view, elementary/basic alternative splicing events (such as exon skipping, alternative 3'/5' splice site...) can be combined into more complex alternative splicing events. If it is possible, how common is it?
Just to clarify my question, let A->B->C be a transcript made up by three exons (A, B and C). Biologically, is it possible to obtain a new transcript A'->C in which exon B has been skipped (exon skipping event) and exon A has been "cut" at a different splice site producing A' (for instance, alternative 5' splice site event)? Can I obtain also A->C' (exon skipping of B and alternative 3' splice site of C)? Another example could be the following one. Le A->B->-C->D be a transcript. Can I obtain a transcript A'->B'->D?
From a combinatorial point of view, I can combine all the events and all the exons in many different ways but from a biological point of view, are all the possible combinations plausible?
If so, can you please point me to some articles describing how alternative splicing events can be combined?
Thank you and sorry if this has been asked and answered already (but I didn't find anything regarding it).

This is a good question. I cannot see any biological mechanistic reason why the combination you suggest could not occur, but unfortunately I cannot provide you with an example. The literature on the subject looks very complex (e.g. see http://www.nature.com/nbt/journal/v22/n5/pdf/nbt964.pdf), so you really need help from someone in the field.


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Is there any evidence for the validity of RNA/DNA supplements?
Is there any evidence for the validity of RNA/DNA supplements?
I've recently been seeing advertisements for RNA and DNA health supplements in the form of a pill, which claim to perform some rather miraculous functions within the body, though I can find no scientific validity behind this. There are some very respectable companies including Holland and Barrett selling this stuff and I can't see how this would provide any health benefits.
Are there any studies on this? If not, may someone care to speculate if there could be any health benefits to RNA/DNA supplements or is this just a terrible gimmick?

I skimmed through this website and couldn't help but laugh at this: Results of a bold new study from Kashkow University’s School of DNA and Medicine, expected to begin next year, were announced yesterday. They have been called a “breakthrough” and a “game-changer” by some of the leading scientists on the proposed study. Aside from the fact that it makes no sense... Kashkow University?

haha! Brilliant. I especially remark at the comments of Cyrus Tosine

Says it all really. I'm just looking for any particular papers that conclusively refute it as idiots are being taken advantage of

@canadianer Where did you find this blog? It's incredible. Also "Credulity, WI": where people are incredulous? (of course there is no such town, unfortunately - I'd love to live there) "University of California at Boulder" - one of the most covert of all University of California schools... And where Cyrus Tosine is about to say it could help people "concen" ---trate? Seems either Cyrus or the author really need this product! Really truly brilliant piece, rivals anything in the Onion.

@Charlie The burden of proof is on the claimant; I don't expect there to be a lot of research based solely on refuting a ludicrous idea.

Yes I suppose. It however bothers me that this is being sold not only in dodgy online markets but stores people should be able to trust.

The website that canadianer linked to is meant to be satirical about these useless supplements. Despite that, comments left on the site still shows people think he's saying DNA/RNA supplements are good. Love his wit!

It didn't take me too long to realise it was satirical


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What made this tiny honeycomb-like structure?

I found this on the ground in Maryland.  I believe the twig is from a tulip poplar tree.  The structure looks like a tiny honeycomb except that the cells are individual tubes rather than a true hexagonal honeycomb shape.  It's one layer deep and wraps completely around the branch.  I assume it was made by some tiny insect, but what?

Many insects lay eggs in tight clusters; because of the shape of the eggs (like honeycomb cells themselves), the cluster looks a bit like a honeycomb.  If you had a high quality macro shot, the eggs might be easier to identify definitively.
Newly hatched Beet Armyworms:

Wheel Bug (Arilus cristatus) Eggs:

Wheel bugs are common in eastern North America, but are confirmed to occupy areas of Mexico and Guatemala.

With wheel bug for size:

My guess is that you found a cluster of Wheel Bug eggs.

Females lay eggs at a low elevation on trees, bushes, twigs, and other objects.[5] Secreted glue serves as an adhesive which maintains the cluster formation of the eggs. - Wikipedia


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What do we mean when we say that a muscle fiber contracts strongly?
Sounds dumb but anyway, i heard that superfast fibers contract more strongly than fast twitch fibers. And i never thought of muscle contraction as something that has a magnitude (i thought of it as "1 or 0" meaning either contracted or not). So lets say we have two fibers, the same length and thickness, if one contracts more than the other does that simply mean that it becomes shorter ?

i'm no expert but try looking up animations on youtube of muscle contraction that may help, here is one https://www.youtube.com/watch?v=GneonFlcZG8


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How urination prior to blood test may give error?

Source: Textbook of  Practical Physiology, 4th Edition

according to it urination within 30 minutes is a precollection factor that may alter the results of blood test.

I am unable to comprehend how urination could affect the blood sample. Urination will just result in excretion of urine already formed and stored in the urinary bladder, so how its loss could lead to error in blood sample?

This is new  to me and rather baffling. I can't imagine how emptying your bladder affects a blood test. The entire first section of the text is about hematology and covers the subjects in a CBC, nothing else.

Please don't post text as a picture. It's harder to read and cannot be searched.

What is being sampled from the blood?

It's just a general guideline. However we mostly do CBC.


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Why only honey bee collects & store honey?
In Insects, most of flying insects like butterfly etc, diet is sucking honey from flowers. none of them store honey except honey bee. Why so ?

Ants can store honey: https://en.wikipedia.org/wiki/Honeypot_ant

Nectar: sugary goodness in a flower. Honey: vitamin enriched food processed from nectar.

Also honeypot ants are not a single species but a group of ant species who have developed honey storing behaviour.

Many different bees also make honey, not just honey bees (Apis species). There are carpenter bees, bumblebees and as Geraldo said, there's honey pot ants.
Only honey bees make any great quantity of honey. The other species make far less and it's a different consistency. Honey bees live in large colonies and honey is stored to feed developing larvae as well as feeding workers and the queen through winter. Other bees are solitary except for a few bumblebee species but their colonies are much smaller - usually less than 50. Bumblebees make far less honey. There's no need to store honey for winter as the queen and workers die in late fall. Only a newly hatched and fertilized queen will survive, hibernating through winter underground. Hence, storing more than the immediate needs of queen, larvae and workers would be pointless.
You mentioned butterflies sipping nectar. A butterfly's lifespan is very brief and only sips nectar to provide energy for fertilization and egg laying. Then, generally, they die. Larvae have been provided for already since the eggs hatch on the appropriate plant leaves as their food.

Its a symbiotic relationship nature has established between honeybees and the vast hundreds and millions of plants that depend on them for pollination.  Honeybees do almost all of the pollination.  You cannot compare the vast proportion of pollination performed by honeybees with all the rest of the pollinating insects combined.
Because of this pollination dependency, nature has provided honeybees with robustness of colony sustainability, survival, and reproduction.  The energy density of honey is very high and it has all the nutrients the bee larvae need to grow into healthy robust adult bees.  The honey is also a great insulator to help prevent the hive from getting too cold in the winter.  Honeybees are the earliest pollinating insects in the spring, right on time for the earliest blooming flowers.  Their communal collaboration and communication teamwork in gathering nectar is astonishing, unique, and well documented.
Without honeybees, we would have to do without fruits and vegetables, which is why scientists are working around the clock to figure out colony collapse disorder.


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Open databases for copy number variations similar to TCGA
The Cancer Genome Atlas(TCGA) has open data for copy number variation(CNV) from at least 10k different cancer patients. They offer two types of data, CNV data from tumor and CNV data from normal tissue samples. Is there any other open databases that offer CNV data from at least one cancer type?

The ICGC has CNV data for many different cancer types. It has many both restricted and open data sets. The DCC releases page will let you hunt through them - those that are public are easily downloaded. They also have matched expression, SNV, DNA methylation, and structural mutation data for many samples.


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Can I grow unlimited stem cells from limited embryonic stem cells?
If I theoretically extract a few embryonic stem cells from the embryo and cultured in vitro with enough nutrient to grow more cells. How many maximum of stem cells can I get?  Do I need to add any compound to inhibit the differentiation progress?

Culturing stem cells (especially embryonic ones) is very tricky - that's why its so hard to clone mammals. Without a lot of care your cells will not survive or differentiate for that matter.

@Nicolai hi! thank you for your reply. If you know anything about this, could you please tell me about the parameters? What do I need to take care? The temperature, nutrients or anything else? Since I'm an engineer, I will create a robot with several sensors to monitor them for me.

Like I said in my comment stem cell culture is a very difficult process, and while people have been doing research on this for about two decades there is still a lot we don't know about stem cells. Additionally working with (human) stem cells can cause a lot of ethic problems and is therefore under strict regulations in most countries.
In principle stem cells will continue to divide until they get a signal o differentiate. In normal embryo development some cells start producing these signals at different stages, and the complete interaction of different signals allows the formation of the organism.
In cell culture one has to make sure that exactly the right signals (which are mostly growth factors) are present in the culture medium, since stem cells can easily die if they do not get any signals.
I don't have any detailed experience or knowledge in working stem cells, but a quick literature search turned up these two papers, which should provide you a good starting point. There's likely a lot more research out there you can look for.

Hi! Thank you for those information. As a first glance at the article you provided and other information that I've found on the internet, it seems possible to grow a lot of stem cells. I still waiting for some answer from experienced researcher in stem cells to give me some more advice and information, thank you again!


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What is the family of this insect caught by my Drosera?
I am currently trying to find out what type of flies are flying around in my home. If they are fruit flies, fungus gnats or something else.
Currently my Droseraa caught one of them and I am currious what species it is.

It is a small fly, like fruits flies and fungus gnats. As seen in the third photo the length is about 1,5 to 2mm (The distance between each line is 1mm).
The location is Stockholm in Sweden (in my apartment).
Could you help me identifying it?

Can you get a closeup of the wing?  With what is visible at the moment, the best anyone can do is suborder.

Thanks for your answer! I have now added a zoomed in picture of the flies wings.

See here: https://biology.meta.stackexchange.com/a/3683/27148 and try to provide location and size information as well.

Thanks for your comment! I have updated with location and size. I have a picture avaible with the fly close to a ruler, but can't add it as I only have 1 in reputation.

@eternitysharp You now have more reputation. I don't know if this is enough to add more pictures.

@bli Thanks! I have now added the third picture showing its size.

This is a Dark-winged fungus gnat (family Sciaridae); the European species of the family are dealt with by Menzel, F.; Mohrig, W., 1999, Revision der paläarktischen Trauermücken (Diptera, Sciaridae) [A Revision of the Palaearctic Black Fungus Gnats (Diptera: Sciaridae)], Studia Dipterologica Supplement, (6):761 pages; copies are sold by Ampyx-Verlag (see http://www.ampyx-verlag.de/lilac_cms/de/4852,,refz,rd,368,2914,12/index.html).  Some species of the family have economic importance, but identification to species usually requires male specimens which must be at least temporarily mounted on microscope slides.

Thanks for your answer! I think I am good enough with just knowing the family. I will change the question from "species" to "family" and then accept your answer.


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Does testosterone weaken the immune system?
I was reading this articles here that states that the higher the blood level of testosterone is, the weaker the immune system gets.
I read another article about testosterone here that focuses on the positive side of high testosterone blood levels and avoids the effects on the immune system.
So my questions is: Does testosterone really weaken the immune system?

this may help http://www.sciencedirect.com/science/article/pii/S0008874915000313?via%3Dihub


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I really need some help with a plant identification
I am trying to identify this flower. It was spotted in an Australian Botanic Gardens. I have been advised that the plant was approx 1.8m high and the flowers approx 2cm wide. Any help greatly appreciated.

That's an Apocynaceae, from the species Strophanthus speciosus. Its common name here in Australia is corkscrew flower or poison rope.
It's not native to Australia, though: it's native to Africa.
You can easily identify it by the flower:

Flowers of Strophanthus speciosus in the Royal Botanic Gardens Victoria, Melbourne (source of the image)

I would just like to send my sincere thanks for your help Gerardo. I appreciate it very much.

Ann, please consider accepting Gerardo's answer as correct if you think the case is settled.

@Sudachi Thanks for the comment, but this is OP's first question. According to my experience at StackOverflow, OP is probably not going to see this comment anyway... most of 1-question wonders never come back or simply open a new account when they want to make another question.

Yes, I see it quite often. Wish sometimes these could be voted on to close them. It was nice of her to thank you so I thought she might be able log back in and accept the answer. I'll keep my fingers crossed.

Yes, indeed. But that's the policy of all SE sites, we cannot force OP to do anything: accept an answer, upvote, downvote, whatever. I'm used to it: in my last ten answers I have more than 140 upvotes, but no one was accepted.

My sincere apologies If I have failed to do what was expected. I really am so sorry! This is indeed my first time here, I logged in from facebook but I shall be starting an account here if that is OK. I do not know how much I can give to the community but I shall do whatever I can. Sudachi, could you please advise me on how to 'accept' Gerardo's answer? I would be most grateful.

It is fine, I can see now what I should have clicked on. I am truly sorry Gerardo for that! I was incredibly grateful for you identifying that plant for me. I do floral photography and sometimes plants are wrongly identified or not named at all. It can get quite frustrating at times. I owned a plant nursery for many years so have a fair knowledge of local plants but some I still struggle with sadly!

No worries @AnnElliott, that's not a big deal! Next time you need help regarding identification just add the tag species-identification to your question, people here like those challenges, they are like little puzzles.