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What's the name of this bird species?

What's the name of this bird's species, please?

Welcome. By the looks of it, it's a species of sea eagle. To allow users to effectively ID this specimen, they need some additional information, most notably where (and perhaps when) the picture was taken (country, region, season), and what the approximate size of the animal is.

http://www.oiseaux-birds.com/article-fish-eagles-feeding-behaviour.html; guessing bald eagle because of habitat (north temperate?) and white restricted to head (not breast ...)

Is this your picture, or one you found on the web, like here?  Because it would probably be best to give attribution in the latter case.  Thanks!

Please [edit] your post with the location of the picture and an approximate size of the eagle. See [tag:species-identification] for guidelines for asking ID questions here. Thanks!

I would say that it is a bald eagle.  I did a search for similar birds but nothing quite matches the build and coloration.  The bird in question appears to be drying out after being in the water.  On the coast of British Columbia they often feed on fish caught from the water's surface and occasionally get a bit damper than they expect, they then have to dry out like the one in your image.  See the following sites: From Cornell University's site about birds

Welcome to Biology.SE! You are more likely to get a positive response to your answer if you explain in more detail why your identification is correct. Specifically, please edit your answer to add discussion of key features that allow you to distinguish this from the several other very similar species of sea eagle. Without this your answer is indistinguishable from opinion. ——— You may also wish to take the [tour] and then consult the help pages for additional advice on [Answer] effectively on this site. Thank you!

Sure looks like a Golden Eagle to me , white head and tail ( North America).

Golden eagle with a white head ?  If I saw this in N America I would say it was a bald eagle.

You are more likely to get a positive response to your answer if you explain why your identification is correct. Specifically, please edit your answer to add discussion of key features that led you to this conclusion and supporting references or at least validated images. Without this your answer is indistinguishable from opinion. In addition, please address the fact that this looks much more like a species of sea eagle. ——— You may also wish to take the [tour] and then consult the help pages for additional advice on [Answer] effectively on this site. Thank you!

I am absolutely wrong; don't know what I was thinking.

I may be uninvited from the Christmas bird count which will be in our area Saturday.

No big deal — we all have "brain farts" (or at least I doubt you and my entire family are the only sufferers). ——— You do know that you can [edit] (or if you don't think this question is worth the extra work delete) your post right?


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Why are superantigens not "MHC-restricted", and what's the significance?
MHC restriction is the requirement to recognize an antigen in association with a self-MHC molecule; CD4+ cells can only respond to an antigen if it's presented with a self-MHC II molecule, and the same goes for CD8+ cells and self-MHC I.
Various sources say that super antigens require an MHCII+ antigen presenting cell to activate a T-cell, but they're not MHC-restricted. I've found one "clarification" on what this could mean, and it's that various MHC II molecules can present a superantigen. Does this mean that MHC II from different hosts can activate a clone of T-cells if a superantigen is involved? What's the significance of that in a single host, e.g., someone infected by a microbe that produces one of these things?

It means they bind outside the groove, and so bind nonspecifically. This is why they cause such a massive immune response. They activate indiscriminately (i.e., not a clone). I may have time to write this up in full later.

By “non-specifically” do you mean in regards to the paratope the T-cell possesses or the MHC haplotypes/alleles that can present it? I think it can do both, but it’s not very clear to me yet.

What's your understanding of how a T cell clone is activated by a normal antigen? What binds to what?

A normal antigen must first get engulfed by an APC, processes then presented on the surface of the APC. To activate a T cell clone, TCR must bind to an antigen-MHC II complex, and some co-stimulation is also needed: CD4 and MHC II, CD28 and B7, LFA-1 and ICAM1. What I understand from superantigens is that they skip the whole engulfment thing (engulfment and processing makes them lose their "super", rather) and bind to the V-beta part of the TCR and the MHC II outside it's peptide-binding groove, so TCR antigen-specificity is rendered irrelevant.

I think different MHC II isoforms bind different peptides, so you need a variety of those to bind a good number of peptides, and conversely, a particular peptide WONT get presented by every MHC II isoform. Superantigens also skip this particular restriction too, right? Is that what the whole "Not MHC-restricted" thing is about? @DeNovo

Yep, you got it. I would suggest you convert to an answer and I'll upvote.

Dope. Thanks for the help, I'll do that now.

Normal, "non-super" antigens activate T-cells in the following manner: they are first engulfed and processed by a professional antigen presenting cell (APC), e.g., a macrophage. The processed antigen is then presented along with an MHC class II molecule on the surface of this cell. The T-cell's T Cell Receptor (TCR) then binds this complex; it must be able to recognize both the MHC class II and the antigen, and in addition to this "main signal" other co-simulatory signals are also needed. The important thing to remember is that a T-cell will only react to a specific antigen it's specific with when it's present with an MHC class II molecule it can recognize. This is known as MHC restriction
A person has 3 genes (each having 2 alleles,for a total of 6 alleles) for MHC class I: HLA A, B and C, and 3 genes for MHC class II: HLA DR, DQ and DP. These alleles are highly polymorphic, i.e., varied, with each of these 6 genes having hundreds or thousands of different alleles, and the combination of alleles differs from individual to individual; it's very unlikely that two people who aren't identical twins would have the same combination of HLA alleles.
MHC molecules can only bind peptides, and in addition, they cant bind ALL peptides; of all the peptides that can possibly be bound by an MHC molecule, a particular MHC molecule can only bind a select number of those peptides. Different MHC molecular forms, be they class I or II, can bind, and thus present, a different set of peptides. Having different HLA alleles at your immune system's disposal means there's a larger pool of possible peptides your APCs can present with the different MHC class II isoforms they have, allowing defense against a larger pool of antigens.
A normal antigen has 2 "restrictions" on its ability to activate a T-cell clone: it must be presented by an MHC class II isoform that can bind it, and it must be recognized by a T-cell with a compatible TCR.
Superantigens activate T-cells in an unconventional manner: They have a domain that binds to the TCR, though not at the usual antigen binding site, and a domain that binds to the MHC class II molecule, but not in the usual peptide-binding site these molecules possess. Since it binds outside of these regions that are specific to particular molecules, they're not restricted by the antigen specificity of the TCR nor are they restricted by the MHC class II isoform they're utilizing. Hence why, even if they do need MHC class II-positive cells to be able to activate a T-cell clone, they're not MHC-restricted.
Readings:

Immunobiology by Charles Janeway, Sections 5-13, 5-15 and 5-16.

Just add references and you're done! A general textbook level reference will suffice.

Refering to "MHC class II isoform": does every cell, or, every cell type have a different MHC complex (are the proteins homologues)?

source: Stack Exchange

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

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

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

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

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

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

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

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How hard is it to build a promotor in a DNA that initiates DNA transcription when specific hormones are around
I have an idea that you could find out which substances are within a sample in vitro that you are investigating by creating DNA that has a bunch of different promotors for different substances you are interested in.
After inserting those DNA strains you could do nucleotide sequencing and as nucleotide sequencing allows you to to read a lot of data you could read the sequencing behind the promotors.
How complicated would it be to build DNA with promotors for dozens of medically relevant substances?

What do you mean by within a "probe"? Do you mean "sample"?   2) Are you thinking of these detector DNA molecules as being within an organism or in vitro?   3) Also note that typically when this type of experiment is done we would look at protein readouts since proteins can be fluorescent or have enzymatic activities that are easily measured. Is there some reason you want to do a sequencing based measurement and if so why do you think that would be preferable to just doing a standard test e.g. one based on antibodies?

@tyersome : I mean in vitro. You can't measure dozens or hundreds of different fluorescent proteins at the same time on the other hand if you have working promotors you could detect many targets at the same time. The cost of antibody based detection has stayed relatively constant over the last decades while nucleotide sequencing is a technique that fell a lot in price and there's hope of further price drops even if it doesn't fall faster then Moore's law anymore.

Dozens of fluorescent proteins might be possible, but I agree hundreds would be right out. —— I don't want to be a wet blanket, but are you familiar with what transcription involves? Transcription requires multiple components — doing this in vitro would require a mixture including: DNA, transcription factors§, RNA polymerase, and ribonucleotides. All of these macromolecules are subject to degradation and would typically be stored separately at -20°C before mixing. ——— §Note: For each hormone you would need a specific transcription factor that respond to that hormone and bound one promoter.

Promoters bind transcription factors (TFs) and RNA polymerase (or a related complex, in the case of eukaryotes).
The substances you are interested in testing would need to bind to DNA in the same way as TFs and RNA polymerase, in order to trigger RNA synthesis (which you might measure with RNA-seq experiments). That would seem to severely limit what you can test the presence of.
In any case, if you could make that happen for your substances of interest, you would probably also want to make sure to avoid degradation effects of short-length RNA, by removing associated proteins.
https://en.m.wikipedia.org/wiki/Promoter_(genetics)
https://en.m.wikipedia.org/wiki/RNA-Seq
https://en.m.wikipedia.org/wiki/Small_RNA


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Was Dr. Livesey's treatment a valid one in the Treasure Islands?
Here is that incident from Treasure Island by Robert Louis Stevenson, where Billy Bones had a 'minor' heart attack or a stroke (according to R.L. Stevenson).
To give a little background about Billy Bones, he was a pirate, a toughened and hardened person who has gone through the deadly and unethical ordeals of life. He was an alcoholic and used to drink rum a lot. Dr. Livesey had previously warned him of taking any rum at all. But its quite a daunting task to let go a life long bad habit. Another thing worthy to be mentioned is that (to me it felt) Billy Bones had a very short temper which is indicative that he is a very likely candidate of high blood pressure.
In one incident, Billy Bones had a fight with an old foe of him. His foe escaped after collecting some major injuries caused by Billy Bones namely known as the Captain in Admiral Benbow inn. As the fugitive left the vicinity, Billy Bones gasping called out for rum and immediately he fainted.

I heard a loud fall in the parlour, and running in, beheld the captain lying full length upon the floor. ...He was breathing very loud and hard, but his eyes were closed and his face a horrible colour.

Jim called in Dr. Livesey downstairs who was treating Jim's father upstairs.

“Oh, doctor,” we cried, “what shall we do? Where is he wounded?”
“Wounded? A fiddle-stick's end!” said Dr. Livesey. “No more wounded
  than you or I. The man has had a stroke, as I warned him... I must do my best to save this fellow's terribly worthless life; Jim, you get me a basin.”
When I got back with the basin, the doctor had already ripped up the captain's sleeve and exposed his great sinewy arm. It was tattooed in several places...
“Prophetic,” said the doctor, touching this picture with his finger.
  “And now, Master Billy Bones, if that be your name, we'll have a look
  at the colour of your blood. Jim,” he said, “are you afraid of blood?”
“No, sir,” said I.
“Well, then,” said he, “you hold the basin”; and with that he took his lancet and opened a vein.

My question is about Dr. Livesey's little surgery. R.L. Stevenson writes after this 'surgery',

A great deal of blood was taken before the captain opened his eyes and looked mistily about him.

It almost had an immediate positive effect on the patient. My question is about Dr. Livesey's little surgery. What did he do here? Was it any form of valid treatment?

Welcome to Biology.SE! Thank you for taking the [tour], but please also go through the help pages starting with [Ask] questions effectively on this site. ——— I think this question is too speculative for this site since answers to it will necessarily be "primarily opinion-based". You might want to investigate whether this is an acceptable question for [medicalsciences.se]. In addition, we encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). Thanks!

@tyersome This question is only primarily opinion based to people who aren't familiar with the topic, which is perhaps more about history than biology.

@DeNovo — Since the question is based on event in a work of fiction, there can be no criteria for declaring an answer "correct". Therefore I can't see how this question (as written) could get an answer that was anything other than opinion based speculation ...

OP, are you interested in whether venesection is currently a valid treatment for stroke, or whether it was when treasure island was written or set?

@tyersome The question is about whether venesection is an appropriate treatment for stroke, which is readily answered. The primarily opinion based close is often an "I'm not familiar with the topic" close. A common mistake. Biological is a broad field. I wouldn't worry about it.

@DeNovo — Your question to the OP could guide them towards making this a valid question, but that doesn't mean that it is answerable in its current form, which is focused on fictitious events.

Let us continue this discussion in chat.

@De Novo, what was that word? 'venesection'? Thanks a lot. I'm only interested about the treatment. That's it. I guess my question phrases it clearly.

@Ahmed yes, venesection, the procedure described by "he took his lancet and opened a vein". Are you interested in whether that is currently a valid treatment for a stroke, or whether it was back when the book was written or set. Those are separate questions.

The procedure described here is called venesection. It is no longer standard of care, but was when Treasure Island was written.
Here is an excerpt from the first edition of Cecil's Textbook of Medicine (1927):

During the acute apoplectic attack the following therapy may be employed: The patient should be put to bed with the head elevated. If he has fallen to the ground the clothing around the neck must be loosened. Difficulty in swallowing contraindicates the administration of nourishment by mouth. An enema may be given. When the face is puffy, the pulse full and strong, and there is reason to suspect hemorrhage, venesection is advisable. It should be employed only for plethoric individuals, not for patients who seem asthenic or arouse suspicion of thrombosis. Usually 250 to 300 cc. of blood are removed.


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Vision: what is the difference between on-off ganglion cells and lateral inhibition?
Is 'lateral inhibition' just a term for the biological basis of the functioning of the on-center (or off-center) ganglion cells?
Or do these terms describe separate processes?

Short answer
Retinal center-surround receptive fields are an example of lateral inhibition. It occurs elsewhere in the nervous system too.
Background
Center-surround receptive fields are indeed an example of lateral inhibition, where the ON field suppress the OFF field through lateral inhibition. The center-surround connectivity in the retina (Fig. 1) is indeed the most well-known example of this kind of circuitry. However, lateral inhibition occurs in other sensory systems too, for example auditory and olfactory neurons (Bakshi & Ghosh, 2017). For more information on the retinal circuitry underlying center/surround inhibition see this answer.
References
- Bakshi & Ghosh (2017), Handbook of Neural Computation: 487-513.

Fig. 1. Retinal circuitry underlying On-OFF center-surround conncetivity in ganglion cells. source: New York University


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Neuron stimulation experiments
Has anyone extracted a class of neurons (or a connected set of neurons) and stimulated them electrically to get an understanding of their behavior?
If so, could someone point me to papers along these lines? If not, do people have an idea of why this is not been technically feasible yet? As I would imagine this would be tremendously useful in building neuron models.

Have you heard of optogenetics? For single neurons though there are classic experiments involving electrical stimulation. To me it seems like this question lacks any background study which makes it impossible to answer reasonably.

Short answer
Although outside my direct area of expertise, there is quite a lot of literature on the topic. The trick often is to use the correct keywords. Key in "recording + stimulating + ensemble + neurons", or "Utah + neuron + implant".
Background
There is quite some literature on this topic. For instance, a much used device in this arena is the Utah implant (Fig. 1), which can be used to record and also stimulate neurons (e.g., Nordhausen et al. (1994)). It has 100 penetrating electrodes and is even used in humans. There are also other approaches, e.g. by implanting a bunch of microwires (e.g., Nocolelis et al (1997)). In scientific jargon, the recording of multiple neurons simultaneously is often referred to as 'ensemble recording' (Nicolelis, 2008).

Fig. 1. Utah Implant. Source: WebVision
References
- Fernandez & Normann, Introduction to Visual Prostheses. In: WebVision, online book
- Nicolelis, Methods for Neural Ensemble Recordings, 2nd ed., Front Neurosci, CRC Press/Taylor & Francis; 2008
- Nicolelis et al. Neuron (1997); 18(4): 529-37
- Nordhausen et al., Brain Res (1994); 637: 27-36


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How much does 10g of glucose raise the blood glucose level?
If you would calculate it:
~5 liters of blood = 50 deciliters
10g glucose = 10000 milligram
so the glucose level raises by 10000mg/50dl = 200mg/dl
However, it is known that ingesting 10g glucose only raises the blood glucose level by ~40mg/dl
Why?

@rotaredom I was talking about putting the glucose in through ingestion, that probably solves the problem. thanks!

This is nearly a personal medical question, since you're asking about your blood glucose level, but it does seem like your interested in the physiology here. I'd suggest depersonalizing this question, doing a little more research, and clarifying the actual physiology question here. To point you in the right direction, you might ask yourself how plasma concentration in a living organism is different from concentration in a beaker.

@DeNovo the 40mg/dl are actually not personal, it's an average of most diabetics.

The "I" statements are a problem, and the statement of personal experience. If you depersonalize, you'll be more likely to get an authoritative answer

If you get an intravenous injection containing 10 g of glucose, all glucose will enter the blood within few seconds and your blood glucose level will temporary rise by ~200 mg/dL.
If you take 10 g of glucose by mouth, the glucose will be dissolved and distributed within the stomach and small intestine and will be gradually absorbed into the blood, let's say within 30 minutes. In this time, some glucose will already move from the blood into the cells, so you will never have 10 g of additional glucose in the blood at a given time.
The actual blood glucose rise after ingestion of 10 g of glucose is not a fixed number, but a range that depends on several factors:

The gastrointestinal tract plays a major role in the regulation of
  postprandial glucose profiles. Gastric emptying is a highly regulated
  process, which normally ensures a limited and fairly constant delivery
  of nutrients and glucose to the proximal gut. The subsequent digestion
  and absorption of nutrients are associated with the release of a set
  of hormones that feeds back to regulate subsequent gastric emptying
  and regulates the release of insulin, resulting in downregulation of
  hepatic glucose production and deposition of glucose in
  insulin-sensitive tissues. These remarkable mechanisms normally keep
  postprandial glucose excursions low, regardless of the load of glucose
  ingested.** (Role of Gut in Glucose Homeostasis, Diabete Care, 2016)

Not to mention there are other fluid compartments, two other sources of incoming glucose, outgoing glucose through utilization and storage, and  even renal spillage at a certain level, a well as many many gluco-regulatory hormones (beyond insulin) that control these processes, in part, to maintain a narrow window of plasma glucose concentration regardless of acute differences in oral intake.

Even in a fully uncontrolled type 1 diabetic state, with ketoacidosis,  it's not the glucose that gets you into (acute) trouble. It's the fluid shifts, the cerebral edema and hypokalemia. So even without any insulin, the plasma compartment doesn't act like a beaker.


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ID request ~2mm insect monstrosity
This tiny monstrosity (~2mm in length) was inside of some kind of "flat tent cocoon" on a pepper plant leaf in Washington state, USA.
Not sure what's going on here. Is it malformed or infected?

Could you please attach an image of the "cocoon", it should be helpful

@Algae I don't have the image, and now the "cocoon" is destroyed. It looked like a flat round bit of insect silk on the leaf, the insect was in the center under the silk, thus giving it slightly "tent" appearance.

@SergiiDymchenko did the cocoon look like this or like this?

Also, is that "fluffy" lookign stuff in the rear of the insect simply rolled-up "cocoon" or did it appear to be coming out of the insect's abdomen? Could you describe its texture?

@theforestecologist the cocoon looked more like the first example you posted.
The fluffy stuff looked like it was growing from the abdomen, it was rigid and looked a bit like fungus (but probably not fungus). I was suggested elsewhere that this is a failed to develop micromoth pupa, and the stuff is hairy larval skin.

pretty sure its of the hyperorder Hymenopterida, probably Apoidea possibly lepidoptera

It looks like Lepidoptera to me. It did not properly eclose from the cocoon and the wings did not unfold properly before hardening, which is the reason for the odd appearance, but I'm pretty sure I can see some of the anterior wing veins branching in the section facing us.


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Appropriate regeneration of StrepTrap HP columns for FPLC
My question is related to protein purification using a ÄKTA FPLC.
We used StrepTrap HP Columns (1 ml column Volume (CV)) from GE Healthcare Life Sciences to purify a strep-tagged protein. In the first approach, this worked pretty fine.
We wanted to re-use the columns after regenerating them according to the official protocol. The included steps were all performed at a flow rate of 1 ml/min and with filtered solutions:

3 CV distilled water
3 CV 0.5 M NaOH
3 CV distilled water
5 CV 20 % EtOH
Storage of columns in 20 % EtOH at 4°C.
Equilibration of the columns with Binding Buffer just before next use.

By adhering to the protocol we encountered some problems with the next purification (it was the same protein, but a new sample of cell extract). The purification worked less effective and the amount of purified protein was very low.
We tried a slightly different protocol for regeneration, also at a flow rate of 1 ml/min and filtered solutions.

5 CV distilled water
5 CV 20 % EtOH
3 CV 6 M Guanidinhydrochloride (sol.)
5 CV 0.5 M NaOH
3 CV distilled water
5 CV 20 % EtOH
Storage in 20 % EtOH at 4°C
Equilibration with Binding Buffer before next use.

We chose the Guanidinhydrochloride to denaturate all remaining proteins from the column resin and support the regeneration by this.
But also with this protocol we encountered the same problems (low efficiency of purification).
I would be very interested if anyone of you have encountered the same problems and maybe have a solution/better protocol for this regeneration step.
Thank you for your suggests in advance! :)

What was the exact problem with the second purification (eg poor binding, poor elution, etc). Did anything change with the preparation of the second sample? Did you use desthiobiotin for the first elution? Is there a lot of biotin in the culture medium?

We used desthiobiotin (2.5 mM in Binding Buffer (Tris, NaCl, EDTA)) as Elution buffer. The second sample was prepared exactly the same way as the one before (same incubation time, same induction of protein expression). Additionaly we tried it with another protein (with a new column) and observed the same problem. Meaning: First purification was rather good, the second was not so nice. The culture medium contained 0.2 g/l Biotin (CGXII+Glucose). What we observed during the FPLC was, that the peak for the eluted protein was not very high. We are not sure, if this is because of poor binding.

Or because of poor elution. We tested the flowthrough on an SDS-PAGE and it seems in both cases (the first attempt, where the purification was fine, and the one where it was not) that we have enough protein in the sample (strong bands at the expected MW of our protein in the cell extract and still in the flowthrough.).

How much of your target protein is in the flow through compared to the sample that was applied? That should tell you how well it is binding. You might want to think about how much of the biotin in the culture medium is making it to your column. Biotin will bind with very high affinity and prevent binding of the strep-tagged protein. It might be irrelevant but is perhaps worth considering.

Is there a technique to determine the amount of target protein in the cell extract and in the flow through? I guess a BCA Assay e.g. would just give you the amount of total protein in the sample? The remaining Biotin is a very good point I have not thought about at this point! Is a HABA assay an appropriate way to measure the Biotin amount in the sample?

I would just compare the bands on SDS-PAGE. You don’t really need to determine the exact amount that bound but rather just get a rough idea of whether it is binding at all.

HABA binds to streptavidin in the same site where biotin binds, so you could use it in combination with streptavidin to assay biotin concentration. That might be more trouble than it’s worth though. If you are worried about biotin blocking the column, you could instead use HABA to check the column for binding capacity.

You might try contacting customer support before you get too deep into troubleshooting yourself as they may have seen a lot of these problems and have solutions already.

Ah okay, we did this already. What you can observe is, that you have a rather strong band for the cell extract and also for the flow through (we chose a very high induction rate, which is tolerated by the organism). And also for the fraction, where the purified protein should be, you can see a very clear and strong band. We approved, that the protein is in all three samples by Western blotting, where you can see a very nice and clear signal for the purified fraction. This is only for the first attempt with a fresh column, the second run resulted in a much lower signal for the pur. protein.

Yes, I agree with you. The first approach before overextending the tests would be to ask customer support. I was just curious for some ideas or experiences with this problems. I will add it here, if there might be some useful input from the customer support! Thank you very much for your assumptions and ideas :)

There could be a couple of things affecting the binding capacity of the column, but prime suspects would be either damage to the strep-tactin proteins or some sort of irreversible binding occurring. I would contact support and give them all details of your experiment.

I'm starting to suspect we are having issues with the column regeneration too. Did customer support ever get back to you? I've not worked with StrepTraps before, but I'd expect the resin to last more than half a dozen purifications, so I'm working with we haven't managed to elute all the protein from previous runs and all the column is saturated meaning all new proteins flow straight through. It would be great if you could share how you fixed this! Thanks
Abbie


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Regulation of the TCA cycle and glycolysis by adenine nucleotides
Why is the tricarboxylic acid cycle regulated by the ADP/ATP ratio as stated in the following quote :

Isocitrate dehydrogenase is allosterically stimulated by ADP, which enhances the enzyme's affinity for substrates.1

while glycolysis is regulated by AMP/ATP ratio as in the following quote from the same book :

Why is AMP and not ADP the positive regulator of phosphofructokinase? When ATP is being utilized rapidly, the enzyme adenylate kinase (Section 9.4) can form ATP from ADP by the following reaction: 2

I want to check my hypothesis that it is because the TCA cycle needs acetyl-CoA ( which can come from glycolysis and other sources such as beta-oxidation of fatty acids) in order to operate, so it gets acetyl-CoA from many sources and isn't dependent on glycolysis alone, and that's why it is affected by ADP (which increases upon initial exercise) while AMP stimulates glycolysis (increases after more exercise) to give more acetyl-CoA and that's rate of the TCA cycle is faster than glycolysis?
References
1,2 J.M. Berg et al. (2002). Biochemistry, 5th ed. New York: A H Freeman.

I finally found time to provide an answer. It's not short, although I have provided a two-sentence summary. However the situation is extremely complex. I didn't explicitly say that your hypothesis was wrong — it is. The regulation of glycolysis and the TCA cycle energy charge has nothing to do with the particular demands of the muscle as it exists in bacteria and yeast. Regulation of tissue metabolism involves hormonal control of phosphorylation of the enzymes, and as another story in itself.

Summary
Glycolysis and the tricarboxylic acid cycle (TCA cycle) are distinct processes which are not necessarily linked sequentially. It is therefore not surprising that their modes of regulation are not identical and, in fact, involve far more complex regulation than mentioned in the question. The use of AMP rather than ADP as sensor of energy deficit depends on the action of adenylate kinase, which may differ between cytoplasm and mitochondria.
Relationship Between glycolysis and the TCA cycle
The expectation evident in the question that glycolysis and the TCA cycle should be controlled in exactly the same way assumes that either the two processes are inextricably linked or at least that the functioning of the TCA cycle is dependent on that of glycolysis. This is not the case, although the student can be excused this misimpression from the (perhaps unavoidable) way the topics are generally treated sequentially in text books of biochemistry.
The primary function of glycolysis is to produce ATP directly from ADP. The end-product of the pathway, pyruvate, is in some circumstances converted to acetyl CoA for the TCA cycle, and the NADH generated used for production of ATP generation via the electron transport chain (etc) and oxidative phosphorylation. However pyruvate has a variety of other possible fates depending on the type of organism or — in higher organisms — the tissue, and their overall metabolic requirements. For example in anaerobic metabolism — including exercising muscle tissue mentioned by the poster — the pyruvate may be reduced by reactions that regenerate NAD+ from NADH, e.g. conversion to lactate. It can serve as a precursor of the amino acids, alanine, valine and leucine. It can also be converted in the reaction catalysed by pyruvic carboxylase to oxaloacetate, the key intermediate that allows acetyl CoA to enter the TCA cycle. The importance of direct synthesis of oxaloacetate in this way is that it allows continuation of the cycle when intermediates are used for synthetic purposes (discussed below), in which circumstances oxaloacetate becomes depleted.
As regards the TCA cycle, there are sources of acetyl CoA other than pyruvate produced by glycolysis, and it has functions other than energy generation. Acetyl CoA can arise from the breakdown of fatty acids and of certain amino acids. In multicellular organisms, pyruvate can also be produced from lactate taken up from the blood, although in liver cells it is likely to be used for gluconeogenesis. And certain bacteria — acetic acid bacteria such as Acetobacter — can utilize the ethanol produced by fermentation in the TCA cycle. In addition to its function in energy generation some of its intermediates (α-ketoglutarate, succinyl CoA and oxaloacetate) are precursors of biosynthetic pathways, and the production of citrate from acetyl CoA is a means of transferring the latter out of the mitochondrion, where it is reconverted to acetyl CoA by the citrate cleavage enzyme (ATP citrate lyase).
It is therefore not surprising that there will be differences in the regulation of glycolysis and the TCA cycle, and, indeed, that there will be differences between different organisms — something generally not mentioned in elementary texts.
Regulation of Glycolysis
The prime function of glycolysis is the direct generation of ATP (“at the substrate level”), and flux of glucose through it is controlled by the regulatory effects of both ATP (–ve) and AMP (+ve) on phosphofructokinase, which was established and rationalized by D. E. Atkinson (Biochemistry 1968, 7, 11, 4030-4034) in terms of a response to the overall energy charge of the system.

This arises from the ability of adenylate kinase to reconvert ADP to ATP:
               2ADP → ATP + AMP

[from Atkinson and Walton (1967) J. Biol. Chem. 242 3239–3241]
It can be seen that AMP is a much better indicator of low energy charge than ADP in the circumstances represented by the graph above.
Citrate is also a negative effector of the enzyme, providing co-ordination between glycolysis and the TCA cycle. (Hormonal regulation via protein phosphorylation occurs in the tissues of higher eukaryotes.)
Regulation of the conversion of pyruvate to acetyl CoA
In order to enter the TCA cycle, pyruvate needs to be converted to acetyl CoA by the pyruvate dehydrogenase complex. The regulation of this enzyme determines the extent to which this occurs, and, hence, the extent to which pyruvate is metabolized by other processes. Negative regulators here are high concentrations of the reaction products, acetyl CoA and NADH, although in higher eukaryotes hormonally induced protein phosphorylation is important.
Regulation of the TCA cycle
Then first regulatory enzyme of the TCA cycle, isocitrate dehydrogenase, responds to the concentration of the key molecules involved oxidative phosphorylation: it is stimulated by ADP and +, and inhibited by ATP and NADH. It is worth reflecting on the consequences of inhibition. If a build-up of citrate occurs, this can feed back and inhibit phosphofructokinase in glycolysis. However the citrate can move to the cytoplasm of eukaryotes and be converted to acetyl CoA (for fatty acid synthesis) by the citrate cleavage enzyme, which is stimulated by ATP and inhibited by ADP.
A later regulatory stage is α-ketoglutarate dehydrogenase, which is inhibited by ATP, NADH and its product, succinyl CoA. Inhibition of this enzyme would allow a build-up of α-ketoglutarate, which is a precursor of several amino acids.
This the existence of several regulatory steps in pyruvate oxidation and the TCA cycle allows the use of the cycle for both energy generation and as a source of synthetic precursors. Hence it should be evident why its control is similar to that of glycolysis in some respects, but exhibits key differences.

[Berg et al. Biochemistry 5th ed, Figure 17.18]
But why isn’t AMP a regulatory molecule in the TCA cycle?
Glycolysis and the TCA cycle do not need to march in step, although when they are both responding to the need for ATP their key enzymes are regulated by adenine nucleotides, among other molecules. The original question (or a modification of it) remains as to why is AMP a positive effector of phosphofructokinase, but not of isocitrate dehydrogenase, which responds to ADP. It is interesting that in the section of Berg et al. discussing the concept of energy charge, a rather lame rider is added without further explanation to the effect that the ATP/ADP ratio can also act as an index of energy status.
I don’t know for certain, but suspect that the conditions under which Atkinson’s equation for energy charge is valid do not hold in the mitochondrion. This is supported by Sobol et al. (1978) Eur J. Biochem. 87 377–390 who found concentrations of AMP in rat liver mitochondria to be much lower than would be expected from equilibration with ATP and ADP through the adenylate kinase reaction. They suggested additional reaction of AMP with GTP in the mitochondrion might be responsible and also cited reports that adenylate kinase was absent from the matrix of rat liver mitochondria.
At least in rat liver, this would explain AMP would not be a useful regulatory molecule, whereas the ATP/ADP ratio would be indicative of the requirement for oxidative phosphorylation.

I have slightly amended my answer as regards AMP controlling glycolysis but not the TCA cycle. My initial hunch was correct, but the details not. Anyway I think the answer now better addresses this aspect of the question.


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What is the relevance of the constant in the clearance equation?
I have seen the equation for drug half lives described variously as (0.7xVd)/Cl, (0.693xVd)/Cl, and (ln2xVd)/Cl.
What is the origin of this numerical constant in the numerator? What does it signify?

Does this answer your question? Derivation for drug half life

Welcome to Biology.SE! We encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). At a minimum please search on this site for similar questions that have already been asked such as the one suggested by @rotaredom. ——— Please also take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and edit your question accordingly. Thanks!


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Is there any program or website that allows me to create phylogenetic trees without having to insert an already created dataset?
I asked a similar question on Quora before, but did not get any useful answers as the program the one answerer suggested turned out to have the exact same problems as all others I have found so far.
Most programs for the construction of phylogenetic trees—being made for researchers in various biological disciplines—seem to rely on the input of a dataset that is a formulation of collected genetic and/or anatomical data.
Specifically, I am looking for a program that is like this, but with a GUI that allows tree editing (i.e. you can add and remove new taxa), for example, poorly described/novel theoretical species, dubious species, and subspecies and can be used to create simplified versions of charts like these.

Welcome to Biology.SE! Thank you for taking the [tour], but please also go through the help pages starting with [Ask] questions effectively on this site. Note in particular that this doesn't appear to be a question that is appropriate for this forum — a tree without data is fiction not biology. ——— There is a [worldbuilding.se], perhaps that might be an appropriate venue for this question? Thanks!

@tyersome The reason why I first asked this question on here, rather than the Worldbuilding forum was because I was not sure that anyone on there would have the expertise to answer the question, given the fact that the majority of questions deal with fantasy and (relatively) soft sci-fi concepts, and when hard scientific concepts are brought up, they are not usually in the the fields I am looking for.

@tyersome So, do you think I should still try to ask the question there? Also, now that I look back upon it, I feel that a better way of phrasing the question would be that I am looking for a software where you can directly create and edit phylogenetic trees (through an intuitive graphical interface), rather than having to indirectly edit it through the difficult and gratuitous creation and/or modification of a dataset that one must run through the program.

I can't tell you whether Worldbuilding is the right place, but I can assure you that your question doesn't belong here and won't get an answer even if it isn't closed. The problem is that an expert in phylogenetics is unlikely to have an answer because no one studying biology would need to build a tree that wasn't based on data. Consequently, I doubt that anyone has taken the time to create software for that purpose.

I agree it does not belong here but I don't understand why you can't use some general graphics program like inkscape or photoshop or something? At the end of a day you just want to draw a custom picture of a tree, no?

Maybe SoftwareRecs.SE?

@BagiM Something with similar functionalities to that would be perferred, but the problem with those specific programs is that creating a tree that looks professional with them would require a large amount of advance planning, and I would basically have to rip up and redo the entire thing if I were to want to add or move a taxon.

@BryanKrause Thanks, I'll try there.

I should probably stop talking now, sorry for wasting everyone's time.

if you're comfortable programming in R you could easily define your own phylogenetic tree in the ape package.  Alternatively, if you write down your tree in Newick format, a standard and fairly human-friendly format, you could probably import it into any of a number of phylogenetic tools ...

@Grant I disagree. When using vector graphics program like inkscape or illustrator no advance planning would be necessary while keeping professional look. Seamlessly adding or removing taxon should be quite straightforward.

I'm voting to close this question as off-topic because it is not about biology as defined in the help center.

I think this can be a valuable question in the context of lab techniques. I've tweaked the wording of the question to highlight that this might be a valuable question for people sketching out incomplete or weird trees.

Have you ever tried using Mesquite?
I used it when I taught intro bio lab course as a TA.
Basically you try to come up with yes or no questions, and based on how you answer these questions it will generate a tree similar to your second link.
Can be a little bit complicated, but I am sure there are many tutorials for it on its website.


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Fungi in my Solarium - how do I stop it?
Noticed fungi growing in my solarium in a few spots - probably a few spots where moisture is getting in.  It is really tough, like rubber.  Can cut some of it out with a utility knife, but even that was not an easy process.  Couldn't dig all of it out as it has gotten into some little crevices.  How can I treat this?  Tea tree oil or Oil of Oregano, or ?
The type of flooring is Bamboo.
The spotty things you see on the floor are spider droppings.. how that critter got in there is a mystery - room is always closed, way up on the 3rd floor where I never see any spiders, room is hardly used, and no openings for little flies or anything to get in for its food...?  Anyways, I digress... my real concern is to stop this fungi growth!
Thanks in advance...

Welcome to Biology.SE! Are you sure this fungi and not some sort of overzealously applied sealant? If you are sure it is fungal, does it have any odor? ——— Please also take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and edit your question accordingly. Thanks!

Yes, definitely fungi.  I put the floors in myself, and this area is inside, and does not need sealant - was not there for 4 years, but this time I checked, I was surprised to see this growth.  It is a bit moist, and does smell like mushrooms...!

I'm thinking that this site is probably not the best place for this question — maybe [diy.se] would be a better fit? ——— That being said, fungi are tough, so I doubt any surface treatment is going be much help. Since fungi generally like moisture I'd check for leaks from outside and inside — also make sure the humidity in the room is being kept reasonably low. After that I think you would want to remove what growth you can (replace the affected floor boards if possible).


text:
Should consciousness be a defining property of living organisms?
High school students in India under the CBSE Board are taught that consciousness is a defining property of living organisms.
This question lies under the topic of 'What defines living organisms?'
Does that mean that if robots and other artificial intelligence have consciousness and can react to some external stimuli (just like plants), they are alive?
Also, what about the patients in coma or those who are 'brain-dead', are they alive or dead?
Then, how do we define living in terms of science?
A possible answer in my opinion to the second question above could be that life begins at conception and an organism is considered alive till the point where it has no differences with the dead; i.e. a person who is 'brain-dead' would still be considered alive because he/she still isn't the same as a dead person.
So should consciousness be a defining property of living organisms?

Edit: Defining Consciousness-
In the NCERT textbook which is used to teach the CBSE high school students in India, consciousness is explained as the ability to sense the surroundings or environment and respond to the environmental stimuli which could be physical, chemical or biological.

For reference: NCERT Class 11 Biology Textbook~ Unit 1: Chapter 1, Page 5 (second paragraph)
Link to book: 1http://ncert.nic.in/textbook/textbook.htm?kebo1=1-22

Define consciousness.  Is a bacterium conscious?  How about a potato?  Seems like an appropriate question for the (insert choice of religion) site.

@jamesqf It is mentioned in the textbook that, 'All organisms, from the prokaryotes to the most complex eukaryotes can sense and respond to environmental cues.' So this should mean that bacteria and potatoes are indeed conscious as they can react to external stimuli.
I've edited the answer and added the link to the book, you can check it out.

Someone in a coma doesn't respond consciously, but their body absolutely continues to sense and respond to stimuli. A brain-dead person can still maintain body temperature, metabolize nutrients, and maintain blood pH, none of which are possible without some kind of feedback loop that requires response to the environment. Consciousness could be a necessary condition of life, but it's certainly not sufficient - my TV isn't "alive" even though it responds to the stimuli of me pressing the buttons on the remote.

As someone who studies consciousness...that definition of consciousness would be a very unusual one in the field.

in my long-ago high school textbook this was defined as "irritability" (i.e., the capability of sensing and responding to changes in the environment). This is mentioned in the Khan Academy materials

@Roger Baker: But in aany semiconductor catalog, I can find a large number of  little pieces of doped silicon that sense environmental cues, and wire up circuits that will respond to them.  Heck, I'm writing this on one such thing: my computer senses the environmental cue of me pressing keys on my keyboard, and responds by drawing characters on the screen.  It senses the environmental cue of CPU temperature, and responds by turning on the CPU fan when it gets too warm,  Does that mean integrated circuits are alive?

@BenBolker Thanks for your input, the linked resource also comes up with the same conclusion: consciousness is not a defining property.

@jamesqf: I'm so glad that you have come to this conclusion because that exactly is my question too. Perhaps, consciousness is not the right property that can define living organisms as opposed to the non-living. Or maybe, we could come up with a better description of what's 'living' and 'non-living' to clear up the confusion.
And conclude that consciousness should NOT be a 'defining' property as mentioned in the textbook.

@Roger Baker: I think the problem is that the authors of that text are using the word consciousness in a way that's far different from general use.  Which is why I think it's really more of a religious question than a scientific one.

Hi and welcome to Bio.SE! No, consciousness should not be the threshold for being living since it only exists in animals, and even then it is very hard to define and measure. Behaviourism is one way of looking at this. I asked a question a while ago about why viruses don't meet the definitions of being alive here which might answer some of the things you are interested in.

I have to mirror Jamesqf here there are many very different definitions of consciousness, many with a lot of baggage attached. which is why a good definition would avoid the word entirely.

tl;dr this is an extremely unusual definition of "consciousness" (I'd be surprised if you can find it in any standard English dictionary). If you prefer, like Humpty Dumpty in Lewis Carroll's Through the Looking Glass, to define words (in this case "consciousness") in any way you want — i.e., as above ("ability to sense the surroundings or environment and respond to the environmental stimuli ..."), then consciousness is indeed one of the defining characteristics of life.
This property is (arguably) necessary, but not sufficient, for life — things can be 'conscious' (respond to stimuli) but not be alive, but they can't be alive if they don't respond to stimuli.
This property is more typically called irritability. The Khan Academy article on "What is Life?" gives this property under the section "Response" (along with the the other properties "Organization", "Metabolism", "Homeostasis", "Growth", "Reproduction", "Evolution"). (You can also find it in lots of biology textbooks in this Google Books search.) The text you refer to uses similar criteria (growth, reproduction, metabolism, cellular organization, 'consciousness').
As Khan Academy also says, it's hard to be precise:

Living organisms have many different properties related to being alive, and it can be hard to decide on the exact set that best defines life

So, to answer your specific examples:

robots respond to stimuli (and, arguably, have organization and metabolisms), but they don't grow or reproduce. If they did, we might call them living organisms.
people who are brain-dead or in a coma still exhibit some degree of response to the environment/irritability. So do dormant seeds, spores, and other "resting stages" of organisms.

There are always edge cases; is a sterile person (or indeed one who can't reproduce because they're in a coma) "alive"? The Khan Academy web page uses a similar example, the case of mules (the infertile hybrid offspring of horses and donkeys), along with several other examples that illustrate some of the more difficult cases (dieocious/gonochoric organisms that are isolated from members of the other sex [can't reproduce, but still considered alive]; fire ["reproduces" but not organized or homeostatic]; crystals [not homeostatic, don't evolve]).

And the edge cases can be even edgier.  Consider HeLa cells https://en.wikipedia.org/wiki/HeLa or women in comas who've been raped by their attendants and become pregnant.

I don't think this answers the question (which I doubt could be answered on stack exchange...). "Life" in biology typically do they have the biological machinery to replicate at the cellular level given enough resources. For almost all life, that comes down to does it have ribosomes.

@jamesqf This is not a fringe case at all. HeLa cells are universally considered an in vivo ("within life") experiment. I don't understand why the rape example would be a fringe case.

The title of the question is not "how do we define life?", but "should consciousness be a defining property of living organisms?" (to which the answer is, "yes, if you define 'consciousness' as ability to respond to changes in the environment)

@James: HeLa cells are a fringe case because they're living cells derived from a person who once was conscious, but who is now dead.  So are the cells "conscious"?  Likewise the brain-dead rape victims.  Not conscious by common definition, but still able to reproduce.

@BenBolker That definition is far too nebulous to be of much use in biology. Your roaring fire in a hearth will leap around when poked, whereas an oak tree wouldn't even flinch if I prodded it twice as hard! Being less pedantic, viruses respond in a very biological manner to their environment. Are they "conscious" in any meaningful way? A much more useful measurable and comparable classification for life is "does it have (active/translating) ribosomes in it"? There isn't really a need to drag any other qualifiers in.

@jamesqf This is starting to sound an awful lot like the definitions of a soul...

My final comment: as I say in my answer above (as do the various sources cited), (1) "response to the environment" is a necessary but not sufficient condition (i.e. 'fire responds to the environment' does not by itself imply fire is alive); (2) the particular environmental changes that organisms respond to vary enormously. Trees respond to changes in light, distribution of nutrients and water in the soil, etc.. I think my post is a reasonable answer to the OP's question; if you disagree you can downvote (if you haven't already); post your own answer; or vote to close the Q.

@BenBolker I think my overall point is that those irritability concepts are too soft, hard to define, and non-comparable between organisms without more qualifiers. I've voted to close the question. I agree that your answer is very reasonable. I just don't think any answer would completely answer this question. A more comprehensive essay on the topic of life is this Science editorial: The Seven Pillars of Life. It reframes the irritability as "adaptability" and "improvisation" I suppose.

@James: Exactly, which is why I say it's a question better suited to religion sites, or maybe philosophy, rather than biology.


text:
How do scientists kill the bacteria they themselves made resistant?
I was reading this article on researching bacteria resistance to silver by removing some of their genes.

Researchers then used "colony-scoring" software to measure the differences in growth and size of each plate's bacterial colony. E. coli strains with genes deleted involved in producing sensitivity, or toxicity, to silver grew larger colonies. Strains with genes deleted involved with resistance grew smaller colonies.

Once you end up with some resistant bacteria and you're done researching it, you can't just flush it down the toilet. How do you safely dispose those colony plates in a way that ensures those bacteria don't get out into the wild and reproduce?

The problem with your search is the word "remove". That's not how we normally describe sterilizing, decontaminating, or cleaning biohazards or killing bacteria, or "safely dispose".  https://www.google.com/search?q=how+do+scientists+sterilize+bacteria+after+experiment  got google to suggest "How do you sterilize a petri dish?" for example.

You are absolutely right, flushing down the toilet (or the sink) or simply throwing them into the normal waste doesn't work for biosafety reasons. And it is also not allowed, depending on the country you would do this in, this can lead to hefty fines.
Biologically contaminated lab waste can be inactivated (=all potential dangerous organisms are destroyed) by two ways: Either by heat or chemically. Which ways is used, depends on the kind of waste.
The most commonly used way is autoclaving, meaning treating the waste with steam at high temperatures at higher pressure. The temperature used here is usually 121°C, the exposure time depends on the volume of the waste, since the temperature needs to be reached and kept for at least 20 minutes. See the references for more details.
Liquid wastes (like culture media) can also be inactivated chemically by adding chlorine bleach to decompose the cells. Bleach can also be used to decontaminate surfaces, although here more often alcoholic solutions (70% Ethanol or Isopropanol) are used. After chemical inactivation, the remaining solutions should not be autoclaved as the emerging fumes are either unhealthy (bleach) or explosive (alcoholic solutions) and this is unnecessary, too.
Liquid wastes can also be autoclaved to inactivate them.
Autoclaving has the main advantage that it is rather simple (put the waste into the autoclave, close it and run a appropriate program), the waste can afterwards simply be discarded as normal waste, which may not be the case for chemically inactivated waste, which may need special precaution for disposal.
References:

Decontamination and Sterilization
Decontamination of laboratory microbiological waste by steam
sterilization.
TECHNIQUES FOR STEAM STERILIZING LABORATORY WASTE
Decontamination of Laboratory Microbiological Wasteby Steam Sterilization

I think the important concept is that they're not really invulnerable like Superman, just that anything that would kill them would also kill a patient infected with them. You can incinerate a petri dish, but not a person.

@Barmar Technically you can, just not a person you want to stay alive. ;)

Obligatory XKCD.  (The point, in case it wasn't clear, is that killing bacteria, even resistant bacteria, is really easy.  The problem is that all the best treatments tend to kill humans too, so they're difficult to apply safely.

There is a third method, rarely used:  gamma irradiation.  You need quite a setup to safely handle this, but it has the advantage that it kills the target without utterly destroying it--useful when you're dealing with BSL-4 stuff as many things can still be learned without the risk of the real thing.

Do NOT bleach the organism and then autoclave it.

@xyz123 Good point, I added it to the answer.

Dumb question because I'm not a biologist: would freezing work too? Why does it have to be heat or chemical means? (I do realize that some bacteria can survive low temperatures though).

@EJoshuaS-ReinstateMonica Because freezing is a good way to actually preserve bacteria. This is routinely done in the lab to make stocks of bacteria you want to keep. Heat/chemicals destroy the structural integrity of the bacteria or at least of important parts of them.

@EJoshuaS-ReinstateMonica You need to break the cell membrane or the organelles of the bacteria for it to be dead. Freezing doesn't break anything apart, it just pushes it further together. Adding heat will lead to expansion or burning or some other chemical reaction (like proteins breaking apart), all of which will usually kill living things. Also, since bacteria are also basically animal cells, you can think of it like cooking or freezing meat. Freezing preserves the meat and cooking will lead to various chemical changes.

@JohnHamilton and Christ - thanks, good points. (In case it's not obvious, I'm not a biologist, hence my dumb question :) ).

@EJoshuaS-ReinstateMonica That's what I assumed, but this is fine. Stackexchange is about asking questions and have them answered :-)

@EJoshuaS-ReinstateMonica "It is not shameful to not know, it is only shameful to not learn." It may not be an exact translation but this is my favorite quote from Ataturk. So, ask away, even if the question seems dumb to you, if you're learning, it's all good.

To address what seems to be the misconception underlying your question:
Killing pathogenic bacteria is not difficult; killing them without harming their (usually human) host is.
This is why antibiotics are so precious:
They are drugs that affect only bacteria¹ – by exploiting properties that are unique to them.
It is usually resistance to antibiotics that we care about in bacteria, because it makes infections with such bacteria more difficult or even impossible to treat.
Once we investigate bacteria in vitro, e.g., in a Petri dish, there is no host that has to survive and thus we have far more options to kill them.
The other answers have listed plenty of methods to do this – which are all lethal to humans as well.

¹ This is of course somewhat simplified: Every drug has a side effect, and so do antibiotics. But their side effects on humans are more lenient than their primary effect on bacteria.

Resistance Is...Reversible?
While people generally don't talk about bacteria losing antibiotic resistance, it does happen, and for a pretty obvious reason: the biochemical tools which confer resistance come at a metabolic/reliability/efficiency cost, or the bacteria would have had the resistance to begin with.  In general, we can assume that bacteria are not adept at dealing with silver toxicity because silver does not occur often enough in their favorite environments.  When you take the bacteria out of a silver-concentrated environment, there is no longer pressure to take extra measures to deal with it, and the resistance can be lost.
A Pound of Flesh
There are many ways to attack microbes, and even more ways for them to respond.  The CDC provides a nice overview of some strategies.
Take fluoroquinolones, for instance.  They kill bacteria by suppressing the enzymes which uncoil DNA.  As you can imagine, this makes for a Very Bad DayTM for the bacteria.  If you're a bacterium, and you end up with some ciproflaxin inside your membrane, the most obvious thing to do is get rid of it.  Some bacteria, like P. aeruginosa, which are resistant to ciproflaxin do just that: they build pumps in their membranes to pump it out.  But as any engineer will tell you, adding new pumps to a system costs both space and energy which could have been used for other things (like finding food, reproducing, etc.), so you wouldn't do this unless you absolutely had to.
How do we know that they actually lose resistance?  Well, we've observed it happening!  We literally know which mutations and gene transfers are necessary to confer various resistances for P. aeruginosa, because wild strains are both resistant and susceptible, depending on their exposure to antibiotics (or laboratory conditions).
Gray Goo
Be glad that biology tends to find the most efficient solutions.  This energy minimization tendency might be characterized as a kind of laziness, but it's really an optimal strategy for allocating your energy where it gives you the most value.  For a microbe, that would be finding food and reproducing.  That means that once the lab-grown freaks escape into the wild, whatever super-powers they gained from our mad scientist experiments are likely to be lost over time, once we stop bathing them in mutagenic toxins.
Unlike nanotechnology-gone-wild, we actually don't have so much to fear from lab-induced antibiotic resistance.  It is the pernicious and casual use of antibiotics in our daily lives that will kill us in the end.  These flow down our drains and into our streams and rivers and evolve those critters night and day, virtually guaranteeing that we will encounter resistant types in the wild.

Interesting answer, but it does not answer the question.

While it doesn't answer the question as asked I think this answer provides important background (+1):  that resistance often does come at a cost for the bacteria and thus resistant bacteria are at a disadvantage compared to "wild-type" when the antibiotic pressure is gone again. (This may look different for induced resistance: induced resistance means that the resistance mechanism/pathway is only expressed if needed)

For a species to completely evolve away from resistance, the resistant ones have to die off. So you need some way of killing resistant bacteria to begin with.

@Chris It was a frame challenge.  OP said "you can't just flush it down the toilet", and I attempted to describe why that's not actually a catastrophic outcome. I think your answer covered the conventional sterilization techniques quite well, so I wanted to offer another perspective.

@Acccumulation Time will do that just fine. No bacterium are observed to be immortal (though certain tumors might be). With each generation (on the order of hours, for many genotypes), the ones which don't carry around the unnecessary weight of resistance mechanisms will slowly gain ground on those that do, via mutation, horizontal gene transfer, etc.

@LawnmowerMan While I agree with cbeleites that there is some useful background in this answer, I don't think the frame challenge is all that useful. "You can't just flush it down the toilet" is not merely an assertion of the OP but a common safety standard imposed by legal and regulatory codes, even for fairly low-risk applications. Although I fully agree with you that casual antibiotic use is far more dangerous than lab-grown resistance introduced to low-risk model organisms, practically we don't permit those lower risks to go unabated.

Resistant to WHAT?
Scientists generally deal with bacteria resistant to some concentration of some particular substance (or combination thereof).
Those strains are still pretty much sensitive to great deal of other substances (e.g. etanol 70%), high temperature (boiling water at normal pressure or higher), etc generic ways to kill bacteria.

Autoclave at 120 degrees Celsius for 30 minutes. [ref]
Don't ever flush biological material, living animals, or anything other than sanitary-code approved waste down the toilet.
The proper way to dispose of used culture material is to sterelize it first, then dispose in sealed bags.

After counting, petri dishes should be secured in a plastic autoclave
  bag and autoclaved prior to disposal.  During multi-day field trips,
  place used petri dishes in plastic autoclave bags, and close the bags
  for transport to the office.  Then, following autoclaving, place the
  closed bags of petri dishes in dumpsters or other containers that will
  be emptied mechanically, to prevent accidental contact with people or
  animals.  Never place petri dishes in motel or office wastebaskets.

On a more budget-restricted level, when I worked in a high school, the science lab tech would take all the old Petri dishes out of a dedicated disposals freezer, and take them to the campus coal fired boiler.
Since the boiler only ran in Winter, there was a lot of stuff to dispose in the first few cold days in Autumn.  As such, the science department scheduled much of this work over winter.   Work involving dissection also produced a lot of biowaste, but that was less-bad and could be disposed of in the general waste (it was the 80s, not a lot of recycling at the time.)
Once the furnace part of the boiler was at temperature, the thing was shuttered (somehow) and the access hatch opened.  The frozen plastic dishes were thrown in, inside either paper or plastic shopping bags for ease of handling, then the hatch was closed and the dampers opened.
As for PPE, it wasn't much of a thing.  Disposable gloves were worn for handling the dishes, and they went into the furnace once the dishes were all gone.
I remember once looking in the furnace when it was cold, before the ashes were raked out.  There was zero trace of any material left behind, even metal items like staples or clips were vapourised.
In short - Burnination


text:
What is the meaning of depth relation and EM in this excerpt?
In the excerpt below from Morphology of Invertebrate Neurons and Synapses

For the better part of a century, conclusions were made largely by matching the depth relations between the terminals of input neurons and the dendrites of their presumed targets; this practice became transferred to arthropods and cephalopods. The practice may be true for particular terminals or dendrites, and in vertebrates, but it has been long gainsaid by many examples in invertebrates. In the particular case of Drosophila, now known from dense reconstructions, EM denies any such simple dichotomy in important details, with many terminals having postsynaptic sites and many dendrites that are presynaptic as well as postsynaptic (Takemura et al., 2008).

I'm having trouble understanding what the acronym "EM" stands for, the author seemed to throw it in without prior definition (my guess is it's some neuroscience jargon). I also don't understand what the author means by "depth relation". Could someone explain to me the two terms assuming a college intro level background in neuroscience?

EM is Electron Microscopy; the definition is found earlier in the passage in the normal form where the whole term is given followed by the abbreviation in quotes; you should look for this in the future.

...suited to connectomic approaches using electron microscopy (EM; Lacalli, 2009).

I'm not super familiar with invertebrate morphology, but from context in terms of "depth relation" they are talking about inferring directions of connectivity based on their locations in EM sections. If you find axon terminals from one cell type and dendrites from another at the same depth, you can infer they are likely connected. The passage explains that this doesn't work well in invertebrates that do not have a axon -> dendrite connectivity pattern. Dendrites synapse on other dendrites, and you can't easily tell what the direction of connectivity is from EM alone.


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What is this fruit found in a market in Uyuni, Bolivia at the end of December 2019? (orange skin, 4cm, white flesh)
What is this fruit found in a market in Uyuni, Bolivia at the end of December 2019?

Fruit diameter: ~4 cm. Seed: large, spherical, black. Flesh: white. Taste: sweet but not as sweet as a lychee.

I found the name: it appears to be Garcinia humilis, known commonly as achachairú or achach:

Garcinia humilis, known commonly as achachairú or achacha, is a small, prolifically-fruiting tree related to the mangosteen. It grows in the southern part of the Amazon basin in the central area of Bolivia, but has recently been planted on a commercial scale in Burdekin, Australia.

That matches the area, appearance and season.


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KRAS gene and K-Ras Mutations
This question pertains to the KRAS wikipedia page, and I just want to double check and clarify my own understanding of how this mutation works in cancer.
It states:

K-Ras protein acts like a switch that is turned on and off by the GTP and GDP molecules.

So if K-Ras is a switch, does that mean that when there is K-Ras mutation, it functions defectively so that it does not shut off? So for example when it binds to GTP and converts it to GDP, KRAS does not shut off regardless of GTP is converted to GDP and this would lead to / cause cancer.
So I guess I have several questions to my reasoning above..

Why does excess conversion of GTP to GDP lead to cancer? Is it because this is specifically pertaining to the the RAS pathway?

When I referenced above "it" is the K-Ras binding event the K-Ras protein binding to GTP then converting to GDP caused by the K-RAS gene not being able to function correctly? I'm just confused if its the K-Ras gene causing the problem or the K-Ras protein being the problem, or is it both?

If K-Ras acts as a molecular switch, how to GEFs/GAPs effect K-Ras mutations? Because I know GEFS activate the conversion of of GTP to GDP, but what is its relationship to KRAS/K-Ras?

In the next line it states:

When the protein is bound to GDP, it does not relay signals to the cell's nucleus.

Is this saying when K-Ras is bound to GDP, that the conversion of GTP to GDP won't ever stop? I kind of just don't understand why this was written or what its relevance is. Or is it simply stating K-Ras can only turn on GTP to convert it in to GDP but not the other way around?

NRAS is indeed a molecular switch, as part of the MAP-Kinase signaltransduction pathway it acts in controling the signal which goes downstream and finally will cause the expression of genes. In the case of NRAS this includes genes for proliferation, which is important for tumors. In principle, this looks like shown on this figure (from here):

RAS (this is the same for all three RAS family members) needs to be activated so it can signal downstream, this happens, when GTP is bound to the protein. Since permanent activation is obviously not a good idea, RAS itself has an intrinsic, but slow GTPase activity, which is activated by GTPase-activating proteins (GAP) and will eventually cleave the terminal phosphate group group from the GTP to make GDP + P. GDP bound RAS is inactive. GDP stays bound to the RAS protein and needs to be exchanged against GTP by Nucleotide Exchange factors (NEF) to activate RAS again.
The general principle is shown in this figure (from here):

Mutations in RAS proteins occur in 98% of the time in three locations (see reference 1): In codons 12, 13 and 61. All three mutation affect the ability of the protein to break down GTP by abolishing the intrinsic GTPase activity by the GAP (see reference 2). This leads to the accumulation of RAS protein which is permanently bound to GTP and therefore activated, subsequently activation transcription of genes for proliferation (amongst others). This process can lead to the formation of cancer.
Your questions:

The conversation of GTP to GDP does not lead to cancer. This process stops the activation of RAS proteins. It is the permanent activation which causes the problems.
You have the mutation in the KRAS gene, which is the origin of the problem. The wrong activation is of course done by the KRAS protein.
GEFs facilitate the exchange of GDP to GTP, the break down of GTP is supported by the GAPs. The mutation hinders the GAP to fulfill their role, so they are useless in the mutated form of the protein.
The other way round. If RAS proteins are bound to GDP, they are rendered inactive, unless a GEF exchanges it again to GTP.

References:

RAS isoforms and mutations in cancer at a glance
Guanosine triphosphatase activating protein (GAP) interacts with the
p21 ras effector binding domain.


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Creating animal models
I was wondering how a scientist in a lab may know which type of animal model to use. I have been looking at the effect of a protein on a disease. And have thought about the ways that’s i know this has been done in other research-
- deletion of gene which encodes for protein
- insert GFP by Gene for protein leaving gene intact
- or insert gfp by gene for protein deleting the gene
However I cannot seem to understand how a scientist decides to choose a certain model?

Hi Beth and welcome to Bio.SE! Could you link the paper you are describing in the experiments, and narrow down the question? Currently, it sounds like you are asking a very broad question about animal experimental design and then describing a molecular biology experiment.

If you look at the definition of a model organism as this can be found on the Nature Homepage, this clarifies quite a lot:

An organism suitable for studying a specific trait, disease, or
  phenomenon, due to its short generation time, characterized genome, or
  similarity to humans; examples are a fly, fish, rodent or pig, whose
  biology is well known and accessible for laboratory studies.

So you want an organism, that:

can be bred in large numbers
has a sufficiently short generation time, so you can analyze several generations of it
is well characterized
sufficiently close to the organism you want to learn more about (mostly: Humans), so the findings can be transfered
can be mutated and has your gene/protein/etc. of interest
has been sequenced completely

Besides this general considerations, practical ones also play a role. If you don't have a fish facility on hand, you will most likely not start using zebrafish as your animal model.
There are certainly more requirements, see one of the references.
References:

Requirements and selection of an animal model.
Selecting appropriate animal models and strains: Making the best use
of research, information and outreach
Basic Principles in Selecting Animal Species for Research Projects


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Are there fungi that are directly beneficial for humans?
It is well known that the human body benefits from a lot of different bacteria - and indeed wouldn't be able to survive without them.
Are there fungi that are beneficial to humans, or even needed directly for surviving?

Welcome to Biology.SE! Are you asking specifically about fungi that are part of our microbiome (i.e. live in or on us) or would an answer extolling the many benefits we obtain from yeast be acceptable?

Thanks @tyersome for the welcome! Both aspects that you mention would be interesting. It's nice you mention yeast: I asked this question because I read about the auto-brewery syndrome where yeast grows in your intestine and if you eat a lot of carbon, the yeast produces alcohol, potentially making you very drunk without having imbibed anything alcoholic

Psilocybin mushrooms are widely considered beneficial, and are currently frontier topics of research in health psychology and neuropharmacology. No doubt countless cultures and ancestors would have agreed with the sentiment. From a scientific point of view, these edible fungi and the resulting effects tend to be overwhelmingly beneficial when administered carefully, and more often than not when administered by total laypersons. Relatively few lasting 'side' effects are ever reported and in fact intake of these mushrooms tend to have longer lasting psychological benefits than most known meds.

@SPr Though I'm in favor of and participate in research into those areas, to say psychedelics are "widely considered beneficial" is quite a stretch. The existing scientific studies are small, typically unblinded, and without true placebo (which is difficult). They are also very promising but certainly not definitive. They are indeed still frontier.

It would have been more prudent of me to say widely as in anthropological widely, as an ever-important practice throughout all (pre)history and across disparate and distant cultures around the globe in all sorts of iterations, dosages, preparations and combinations. I certainly did not mean the ivory tower of academia widely, or tobacco company research widely; they haven't been very trendy there.

Saccharomyces boulardii.
https://en.wikipedia.org/wiki/Saccharomyces_boulardii
S. boulardii is a yeast, closely related to S.cerevesiae (if not the same organism).  There is a lot of solid data showing use of this fungus as a probiotic can help treat or prevent intestinal infections.
Systematic review with meta-analysis: Saccharomyces boulardii in the prevention of antibiotic-associated diarrhoea.

RESULTS:  Twenty-one randomised controlled trials (4780 participants),
  among which 16 were new trials, met the inclusion criteria for this
  updated systematic review. Administration of S. boulardii compared
  with placebo or no treatment reduced the risk of antibiotic-associated
  diarrhoea (as defined by the study investigators) in patients treated
  with antibiotics from 18.7% to 8.5% (risk ratio, RR: 0.47; 95% CI:
  0.38-0.57, number needed to treat, NNT: 10; 95% CI: 9-13). In children, S. boulardii reduced the risk from 20.9% to 8.8% (6
  randomised controlled trials, n=1653, RR: 0.43, 95% CI: 0.3-0.6); in
  adults, from 17.4% to 8.2% (15 randomised controlled trials, n=3114,
  RR: 0.49, 95% CI: 0.38-0.63). Moreover, S. boulardii reduced the risk
  of Clostridium difficile-associated diarrhoea

Humans (mammals in general) are host to a diversity of commensal microorganisms, including fungi. An individual microbial species is "good for you" when it stays where it is supposed to be and plays nicely with the other microbial species. That same microbial species can become "bad for you" when it is in the wrong place or in the wrong amount. Fungi are generally less virulent than bacteria (see Murray Medical Microbiology, Ch 68) so they are less likely to be "bad for you" in general, but the same principle applies.
For bacteria, a good example is an infection of the urinary tract by E. coli. The very same bacteria that peacefully coexists, and indeed provides specific benefits while in the gut, causes disease while in the urinary tract (see Murray Ch 30).
Candida species are a good example for fungi -- commensal in the gut, pathogenic in the bloodstream (Murray Ch 74). C. tropicalis is an interesting species in particular, because, while it can cause a pathogenic fungemia, gut colonization appears to be necessary for secondary lymphoid organ development in mice. Willk's answer provides a good example of a fungal species that can be used to treat human disease. More generally, a well regulated mycobiome (commensal fungi) appears to be associated with human health, dysregulation is associated with human disease. They seem to be particularly important for regulation of inflammation and the immune system. Some of the details are reviewed here.
In summary, yes, fungi are beneficial to mammals in much the same way that bacteria are beneficial. When they are in the right place in the right proportion, they are beneficial.


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Is there a difference between "genetic cross regulation" and "crosstalk"?
What is the difference between genetic cross regulation and crosstalk? I'm a physics major and learning about bioinformatics now. So it might seem trivial to many but from the article "Wanner BL. Minireview. Is cross regulation by phosphorylation of two component response regulator proteins important in bacteria? J Bacteriol 1992; 174:2053-8." I could not find a quantitative way to separate these two kind of gene regulations. Also, I would appreciate if anyone can suggest me something to read for further knowledge on this topic. Thanks!

Welcome to Biology.SE! You may find it helpful to take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site.

When learning about a new area I have found it helpful to start with a relatively accessible and reliable source like Khan Academy. Wikipedia can also be a good starting point and you can then check their references. Online platforms exist called MOOCs that offer free (or very low cost) courses on a wide variety of subjects — two that I am familiar with are Coursera and edX. Finally, textbooks with a good level of detail are also freely available online e.g. from NCBI.

I have never heard of “cross regulation” and it seems to be a term invented by the author of the review you cite, and which has never gained common currency. “Cross-talk” is not a specific regulatory mechanism, but a vague general term for the reciprocal interaction between two systems. As my Irish friend would say, if I wanted to get there, I wouldn’t start from here.

@David I have come across this term while studying some articles on systems biology. And those were very recent. One such article is "Zhou, X., Franklin, R.A., Adler, M., Jacox, J.B., Bailis, W., Shyer, J.A., Flavell, R.A., Mayo, A., Alon, U., and Medzhitov, R. (2018). Circuit Design Features of a Stable Two Cell System. Cell 172, 744-757.e17." So, you are probably right. The author may have coined the term "cross regulation"


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Osmotic pressure
Osmotic pressure is defined as:

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

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

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

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


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Why does absorption (at 260nm) of ssDNA increase with temperature?
In the graph below, I understand why A260 of double stranded DNA would increase with temperature increase, as more of the DNA becomes single stranded (and A260 of ssDNA is higher than that of dsDNA because the aromatic bases are more exposed, which absorb the light).
However, I do not understand why the absorbance of ssDNA also increases... I know that individual nucleotides also absorb more than ssDNA (as shown in "inequality" below), but I doubt that the covalent bonds holding the nucleotides are breaking at 80 degrees centigrade. Would this maybe be the effect of an increase in temperature increasing absorption? (I have read that increase in temperature increases collision of photons hence increases absorbance, but I am not quite sure). Thank you.
"inequality" showing which has higher A260:

single nucleotides > ssDNA/ssRNA > dsDNA

One factor to consider is that "ssDNA" isn't actually a single strand — in most cases it will be a pseudoknot where parts of the strand will pair with other parts sometimes in ways that involve noncanonical base interactions that can lead to three and four strand structures. I would guess that "melting" of these structures is a major contributor to the increase. Will turn this into an answer later when I have time if no else does.

@tyersome It's perhaps just my skeptical side, but I'd have a hard time believing that that accounts for a straight line increase... I'd expect it to follow a similar (though much less pronounced and perhaps left shifted) shape to that which double-strand DNA follows.  That said it's not impossible that the graph is not actually all that representative.  Anyhow I look forward to seeing your answer and sources.

This paper looks at the hydrolysis of DNA during prolonged incubation (up to 36 hours) at 70° C.

Thank you for your insightful answers! I do agree with @rotaredom that if there is melting of stemloops (@tyersome) and other "tertiary" DNA structures within the ssDNA, then this denaturation should also be cooperative, and should follow a similar sigmoidal curve to the dsDNA shown... The paper on hydrolysis (@rotaredom) would mean that there's also single nucleotides, which absorb more. It would make sense in this case if the rate of hydrolysis increases linearly with temperature, as shown in the graph. I'm curious for other interpretations!

The decreased absorbance of dsDNA is in large part due to base stacking interactions. Base stacking still occurs in ssDNA, so I suspect that is why you see a temperature dependence.

It might not have to do with any self-interactions of the ssDNA, but instead to do with interactions between different ssDNA molecules. Just because the strand has no reverse complement doesn't mean it can't have hydrogen bond interactions with other molecules of ssDNA

I suspect this may be a chemical question. Have you checked whether temperature has any effect on the UV absorption of nucleotide bases?

It seems canadianer's intuition is correct --

Base stacking still occurs in ssDNA, so I suspect that is why you see a temperature dependence

-- based on this paper:
Conformational Changes in Single-Strand DNA as a Function of Temperature by SANS
Motivation --
UV absorption-based measurement of DNA melting temperature is reliant on the assumption that the DNA duplex dissociates into the same single-stranded DNA (ssDNA) random coil conformations at all temperatures.  However, calorimetry studies (citations 2 and 3 quoted below) have suggested that temperature-dependent conformational changes occur in ssDNA, too.

Early results from calorimetric studies on the dissociation of a 13-mer DNA duplex have shown, however, that the conformation of the single complementary ssDNA does depend on temperature (2). This was evident in the absolute difference between the heat of dissociation of a 13-mer DNA duplex of 490 kJ mol−1 determined at 74°C determined from differential scanning calorimeter (DSC) measurements and the heat of association of the duplex of −236 kJ mol−1 directly determined at 25°C from batch calorimetry measurements (2). This difference was attributed to the additional thermodynamic contributions from conformational changes in the complementary single strands implied from UV absorption changes upon heating solutions of each of the complementary strands from 25°C to 74°C.
...
More recent results also show a large disparity between the free energies of the dissociation of 10-mer duplexes extrapolated from DSC measurements at high temperature to 25°C and the free energies determined directly from isothermal titration calorimetry measurements on the binding of the single strands of the duplex at this temperature (3). This was again attributed to free energy contributions of the change in the single-strand random coil conformations as the temperature increased from 25°C to the melting temperature of the duplex (3).

Methods --
The authors used a 2 μM solution of 10-mer ssDNA (5′-ATGCTGATGC-3′) in 10 mM sodium phosphate buffer, pH 7.0, containing 0.1 M sodium chloride and 0.1 mM ethylenediaminetetraacetate.  Temperature-dependent changes to this solution were measured by three methods:

Small-angle neutron scattering (SANS) at 10°C increments from 25°C to 80°C.  Normalized scattering data were used to compute the geometry of the ssDNA using the LORES algorithm (PDF).
Optical density measurements (260 nm) between 20°C and 90°C, with a heating rate of 1 K per minute and measurements taken every 30 seconds.
Differential scanning calorimetry with continuous measurements from 5°C to 105°C at 1°C per minute.

Findings and Conclusion --
Taken together, the SANS and calorimetry data suggest that the change in shape of the ssDNA with increasing temperature is due to unstacking of bases, corresponding to an endothermic transition.

... [the ssDNA] undergoes an expansion in the diameter direction that causes a slightly shortened length as the temperature increases from 25°C to 43°C. Then, as the temperature increases further from 43°C to 53°C, it expands in the length direction as the diameter decreases. Finally, the ssDNA increases dramatically both in length and diameter as the temperature is further increased from 53°C to 80°C.
...
These conformational changes correspond to the unstacking of the A and G purines as well as the T and C pyrimidines in 5′-ATGCTGATGC-3′ as the temperature is increased. The unstacking is manifested in molecular motion of the nucleotides in and out of the cylindrical axis (an increase in diameter) and in the stretching of the helix or cylinder (increase in pitch). The increase in the optical density upon melting of the single-strand substantiates the SANS results since the optical density changes indicate exposure of the purine and pyrimidine bases to a more polar (water) environment.

And, as with liliae's figure, the results of the ultraviolet absorbance scan show density increasing with increasing temperature.

Figure 6. Normalized UVM scan of a 2-μM ssDNA solution. The solid line is the least-squares fit of a two-state, A↔B transition model to the data points. The broken horizontal lines are the extrapolated pre- and post-transitional base lines and the broken vertical line indicates the temperature at the midpoint of the transition.

Glad somebody found a paper; great answer.


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Are they bed bugs?
I found these two bugs. I know that my pictures are not fully clear, but could they be bed bugs? One was found on the wall between my bedroom door and the other one trap in a Cochrane trap beside my TV in my living room. So far, I haven't seen any bites on my skin. But, I have to admit that I feel very concerned.

Does this answer your question? Insect identification - Is this a bedbug?

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I did, but I would need more help.

Hi, and welcome!  Would it be possible to post some clearer pictures?  These pictures are not really detailed enough to allow for a positive identification.  Thanks!

I suspect your "Cochrane trap" is a "cockroach trap".

In the cockroach trap is a cockroach. I agree. However for the other (which the unclear picture) I'm still afraid of having to deal with a bed bug. I used permethrin product and the bug almost didn't move at all. If it would have been a cockroach, it should have been killed instantly and fall on the floor, shouldn't it? But I check my bed with a flash flight this night and I saw nothing. No bite either. I'm living in Ottawa. So, today, I've opened my bedroom window. I hope that the cold could slow down a possible infestation.

If you think they're different types of insects, you'll have to provide a clearer picture I'm afraid. The one on the wall doesn't look to me like a bed bug because it doesn't have a clearly defined neck.

Great thank you very much! I hope not to have the opportunity to provide you another picture. But you're reassuring me, and I'm very grateful to you. I checked my bed sheet and there's still no trace of bed bugs. I'm keeping my eyes widely opened and I will share with you if there's something new. Thanks'once again.

They look to me like cockroach nymphs (newly hatched cockroaches). Note the long antennae (more than body length) and the two short protuberances at the rear. Also note that bed bugs have a head distinct from the body, whereas cockroaches have a head that blends into the body.
3 mm cockroach nymph (from Wikipedia)

A bed bug (from Wikipedia)

See also this Q&A on What's That Bug.