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Do animals with their eyes ~180 degrees apart have depth perception?
Lots of animals have their eyes more on the side of their head, like an octopus or a parrot. Are animals with eyes more on the side able to tell the depth of objects at different distances? It seems like the line of sight in each eye wouldn't be able to cross to a singular point to triangulate distance.

Good examples of animals with eyes 180 degrees apart are the hammerhead sharks. Here is a good read with very clear illustrations, explanations and quantification across sister taxa. And to address your question, the fields of view of each eye must overlap to produce stereoscopic, binocular vision that allows for (instantaneous) depth-perception. This is called stereopsis. However, many animals perceive depth through head turning - parallax and holding images for comparison - but this is obviously not instantaneous, nor as accurate..!

Yes. Animals can also calculate the distance to object based on the senses of smell, color, and hearing.

Nope, depth perception specifically refers to sight. https://en.wikipedia.org/wiki/Depth_perception but depth sensation would qualify that.

hammerhead vision actually overlaps on the front and back, so in theory they have two different depth perceptions.

Worth noting, even you can perceive depth with one eye closed if you slide your head left and right. It's the same reason we can have 3d gifs that just rely on sliding the camera. Look up stereoscopic 3d lke these:

Welcome. tanks for your nicely illustrated answer. Can you add some references to your answer, and can you add web links to the images you shared? It allows people to background read on your material. +1

Many such creatures do overlap in part of their field of view. Some don't.   Presumably, the former still have some range sense. It's generally accepted that range judgment it's far more valuable to predators while herbivores focus on movement over a wide range. (at least in the sources I've read on this.)
That said:
Focal length can provide some amount of depth information, but not like comparing two angles. ("accommodation " in the wiki article on depth perception)
Parallax can provide some useful depth information. This is a function of basoc geometry. (In the same article, see "motion parallax", "occultation", and "perspective")
Theoretically, if a creature is precisely enough aware of its movement, it could pick up depth by rotating its head. This is because of the previously mentioned geometry. (https://en.wikipedia.org/wiki/Depth_perception#cite_note-5)
Not sure if any animals actually do this, but some birds seem to.

This answer is, fundamentally, just a summary of elementary information. The wiki entry on depth perception chops up the list of factors a lot more fine than I did off the top of my head.
https://en.wikipedia.org/wiki/Depth_perception
https://en.wikipedia.org/wiki/Equine_vision#Visual_field

The rotating of the head in order to improve depth perception is pretty common amongst prey animals.  I have seen this countless times in lab rats of nervous disposition.  When you have them in a box with an open top and are moving around above them, it is very common for the rat to crane its neck so that one eye is looking up at you and then start rolling its head back and forth, presumably to improve its ability to see when you are moving toward and away from it.  As you mentioned, birds do the same thing, and do so even when not under stress, whereas I've only seen stressed out rats do it.

True. My uncertainty is whether that's figuring distance. I'm not sure how you'd test that, but it sure seems likely. I'd sure be interested in any clever studies that demonstrated or disproved this, since I'm not aware of any.

Hmm.  That's an interesting question.  I suppose I just never thought too much about it.  Depth perception improvement just always seemed like the obvious reason for that behavior whenever I've observed it.  I just looked more into it.  There doesn't appear to be any rigorous study of this behavior.  Rats have often been observed doing this same thing before jumping long distances and albino rats with poorer vision roll their heads more often than dark-eyed rats so this seems to lend some credence to the depth perception hypothesis in their case.

Birds seem to be more complicated and have a number of reasons for head rolling, including the inability to move their eyes and the existence of two fovea, which allow switching between binocular and monocular vision.  Interesting stuff.

I didn't know that any birds had multiple fovea. That's interesting. I'll have to look deeper into this. Yeah, that rat note really is pretty compelling, albeit not proof.

In the paper "Rats Maintain an Overhead Binocular Field at the Expense of Constant Fusion", the authors monitor rats eyes while they are doing a task that definitely required visual depth perception: jumping across a gap. A more accessible write up is here. As @the-nate stated, you don't need overlapping visual fields for depth perception. Another depth cue, which he didn't mention, is size. If i know that an object is 1 meter tall, then the visual angle tells me how far away it is.

The size cue is fooled by the Ames room optical illusion.

@Barmar Every system can be fooled. The only question is whether it's sufficiently useful to pay for itself.


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Can someone help me interpret these charts on fluorescent polarization?
I have to present an article about binding designed proteins to fentanyl for my biochem class; I understand everything except how to interpret these charts on fluorescence at the very top of Figure 2a: https://elifesciences.org/articles/28909#fig2
It seems fentanyl was tagged with PE and the proteins (Fen49 and 2QZ3) were tagged with FITC. Fen49 binds with fentanyl and 2QZ3 doesn't but I don't know what about these charts tells me that. Is it the blue specks scattered all over 2QZ3's graph? I'm also confused about the bar graph next to it representing mean fluorescence - does it represent the binding affinities of these proteins/mutations to fentanyl?

These charts are flow cytometry graphs, something not explicitly stated in the figure description, but obvious to everyone who has seen similar graphs before (and I assume it's at least mentioned in the method section of the paper, I didn't read that though).
Each dot in a flow cytometry graph represents a single cell and, as you correctly identified, the PE & FITC flourescence corresponds to fentanyl and the respective proteins of interest. (The labelling was done somewhat indirectly and as is typical for flow cytometry with antibodies but that doesn't matter for the interpretation.). The dots are coloured according to their density: blue indicates only single dots and warmer colors show increased number of overlapping dots (with red being the highest).
It is also important to note that all the axes in these graphs have logarithmic scales, so the shifts you see in the graph represent shifts in orders of magnitude.
The combination of the logarithmic scale with per cell data points means, that you also see 'negative cells' on each axis: along the FITC axis (which represents expression of the protein) you can make out two groups of points. The lower one of these groups has cells that don't express the protein (meaning the florescence detected is just background from staining), while the higher groups contains cells that do express the protein (the staining for the protein is significantly above background).
If you now compare the two proteins you can see that high (protein expressing) group for Fen49 also has an increased signal for PE (which represents fentanyl), meaning that these cells bind fentanyl. In contrast with that for 2QZ3 the fentanyl signal is independent of whether the cells have a low signal or high signal for protein expression.
The bar graph on the right gives the average PE (fentanyl) levels for other additional protein variants. The figure description doesn't explicitly say whether this is the average of all cells or only the ones expressing the corresponding protein at above background levels.

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Why is ATP synthase sometimes referred to as ATPase?
Quite a few times I have seen the term ‘ATPase’ used for what I would consider ATP synthase. For example, my text has:

“The phosphorylation of ADP to ATP is also catalysed by the enzyme ATPase.”

I don’t understand this. Surely the enzyme that catalyses the synthesis of ATP should be entitled ‘ATP synthase’, so why is ‘ATPase’ used in this case?

Welcome to SE Biology. Your question is quite reasonable (I had the same experience years ago) but I have edited it a little to give it a more formal and neutral tone, better suited to the question and answer nature of this site. It is generally useful if you could tell us the name of the texts you quote from, so others can check them.

The way we were
To understand why you may encounter ATP synthase referred to as ATPase, you need to be aware of the historical context — the experimental work that preceded the knowledge of the structure and function of the enzyme complex that we have today. In a nutshell:

Original studies of the components of what we now know to be a complex capable of synthesizing ATP could only be assayed by their ability to hydrolyse ATP. Even though these components (F1 and F1FO) were derived from a mitochondrial system that coupled electron transport to ATP synthesis, and the authors believed these components were responsible for ATP synthesis, they were obliged to refer to them by the activity they had assayed: hence F1 ATPase and F1FO) ATPase.

History lesson
It is instructive to consider a paper by Kagawa and Racker, published in 1966, and entitled:

Partial Resolution of the Enzymes Catalyzing Oxidative Phosphorylation
  VIII. PROPERTIES OF A FACTOR CONFERRING OLIGOMYCIN SENSITIVITY ON MITOCHONDRIAL ADENOSINE TRIPHOSPHATASE”

This work demonstrated that a mitochondrial ‘fraction’ (FO — ‘F’ stood for ‘fraction’) when added to another ‘fraction’ (F1), previously shown to have ATPase activity, could confer sensitivity of the ATPase to inhibition by oligomycin, a compound that inhibits oxidative phosphorylation in intact mitochondria. The title shows clearly that they were aiming to understand ATP synthesis, but were at the stage where all they could measure was the ATPase activity of fractions. It was not until 1973 that Racker and Stoeckenius were first able to  synthesize ATP, and for that they had to use a different system — the light-activated purple membrane of Halobacterium halobium. The key was the incorporation of the membrane — without it there could be no proton gradient to drive the synthesis of ATP, and this was why the isolated F1FO) complex could never catalyse synthesis of ATP on its own.
Those days are gone now
The structure of the components of the ATP synthase finally started emerging in the 1990s, after which no doubt remained that the F1 and FO fractions were part of a synthase.

Therefore, in describing the enzyme complex as we now know it to be,
  there is no excuse to refer to it as anything other than ATP synthase. Moreover there is a particular need to avoid confusion with a membrane ATPase (below).

In my opinion, any textbook that refers to ATP synthase as ATPase is severely out of date and should be burned.
Of course, I exempt historical accounts, as long as the context is made clear.
The acid test
In some cells there are transmembrane complexes, structurally related to the mitochondrial (or bacterial membrane) ATP synthase, that are ATPases. These are the Vacuolar-type H+-ATPases (V-ATPase) which use the energy of ATP hydrolysis to transport hydrogen ions across the membranes of certain tissues and organelles. Another reason not to refer to the ATP synthase as ATPase!

The flagellar motor complex is also a good example of an ATPase that is structurally similar to the ATP synthase.

The right term is ATP synthase, which uses the proton gradient to condense phosphate and ADP into ATP. ATPase is any enzyme that catalyzes ATP hydrolysis into ADP and phosphate, usually coupled with an unfavorable reaction. It should be noted however, that ATP synthase can work in reverse, essentially becoming an ATPase that serves as a proton pump. This could happen with an excess of ATP, but that situation is usually fatal for the cell.
It is common for enzymes to catalyze reversible reactions. In glycolysis for example, 7 out of the 10 reactions needed to produce pyruvate from glucose are reversible. That means that those enzymes are also used in gluconeogenesis, with only the remaining 3 being catalyzed by other enzymes not taking part in glycolysis.

While it's true enzyme names ending with '-ase' usually indicate that this enzyme cleaves a certain molecule, a lot of these names also come from times when people were not aware of the 'natural flow' that the corresponding reactions have. This means that some enzymes (e.g. quite a few in glycolysis) are named for the reverse reaction, compared to the one they perform more often in vivo.

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Methods for microbial identification in soil
I'm trying to perform a survey of the life in a soil sample. I want to know what species of bacteria, fungi, and other organisms are in it. I've heard that ITS sequencing and 16S rRNA sequencing are both possible ways of doing this, but I don't know enough about these techniques to understand which (if either) I should use, or how you interpret the resulting sequence file delivered by the lab. Will these techniques do what I want? How do I choose one over the other? And how do I interpret the results?

16S and ITS techniques try to identify organisms in your samples by amplifying short, 'barcode' sequences from each organism's DNA, and using those short sequences to try to identify the organism they came from.
16S can be useful for distinguishing between prokaryotes (bacteria), at least to genus level.  It will not always give enough information to determine exact species though.  ITS can be particularly useful for distinguishing between some eukaryotes (plants, fungi, etc), even down to species level.  If you are interested in both bacteria and fungi you would need to carry out both analyses on your samples.
A different approach is to use shotgun metagenomics, where rather than amplify only the 16S or ITS region, you extract and sequence any DNA you can from the sample, and then try to assign each sequence read to a species/genus by alignment with a reference collection (e.g. MEGAN pipeline) or by kmer analysis (e.g. Kraken).
There are some packaged approaches for dealing with 16S. Qiime2 is popular, and will likely involve some amount of work in python to get it working.  There is an R package microbiome, but I don't have experience with this.  Mothur is a long-standing stand-alone package that is resonably easy to use, and MG-RAST is a web-based version that is also reasonably easy.
ITS analysis is less fully developed as pipelines, but I am sure you can find some in the literature by searching for other people's studies of soil microbiomes.
This review of techniques and approaches might be helpful if you are interested to learn more about the whole genome/metagenomics approaches: http://ccb.jhu.edu/people/salzberg/docs/Breitwieser-etal-2017-Metagenomics-review-reprint.pdf

16S is still one of the most poplular methods of idenifying organisms. The technique is very well stablish and it works well. However, it has some limitations, for example there is a significant variance of the copy number of these gene in the species. Which makes quantification not very reliable.
To decide which tools are better to analyise your results, you can have a look a the CAMI challenge paper. Several tools for different parts of the analysis are compared across labs. The most popular tools are not always the best for your analysis.


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Is it possible to estimate tree height from stump/breast diameter and species?
Kindly pardon my poor knowledge, my area of expertise is not biology.
I am currently working on project where I have access to tree's stump and breast diameter and its species. We are trying to estimate tree's impact on microclimate on its surrounding.
To simulate it, we need approximation on tree height. So is there a database or textbook I can refer which provide information on estimating tree height from these features?
I understand that there would be no absolute value here but rather a distribution.

Yes and no. Allometric equations exist and are sometimes used. However, they are incredibly finicky - dependent on both species and specific growing area. With soil and water ability varying sometimes at sub-meter levels and known competitive impacts from neighboring trees  likewise depending on species, the ability to  model such allometric equations accurately and precisely is very difficult. This is further complicated by random events (e.g.wind damage, etc.). What are you trying to use this approach for? Most major journals might sneer at the approach given better methods (e.g. Lidar). ..

For southern ( USA) pines; no. In the forest they reach about 100 ft high at less than 2 ft diameter , then the diameter grows to over 4 ft. In an open area they are much shorter.

@blacksmith37 exactly -- under different competition scenarios, trees grow quite drastically different. Remember, trees are fighting for sun and nutrients -- as you alter the availability of one or more  of these resources through environmental shifts or community interactions (e.g., competition) you inherently should expect a shift in size, growth habit, etc.

@theforestecologist: For an example, I was cross-country skiing through a pine forest of mixed age this afternoon (eastern SIerra Nevada), after having read this question in the morning.  Trees with a trunk diameter about 1 ft/25 cm were around 70-80% of the height of ones with a 3 ft/1 m diameter.  And from other observations, younger trees in a dense stand will have tall trunks with few branches until the top, while those growing in an open area will be shorter and bushy, with branches down to the ground.

This is an interesting question for me because my first research internship centered pretty much entirely around this.  It got pretty deep into the weeds as this was a CS, rather than biology, internship and we were mostly analyzing the math behind the allometry (e.g. Log-transformed linear vs. nonlinear regression for fitting the curve, OLS vs. RMA regression, traditional vs. monte carlo methods for comparing curves with different numbers of parameters, etc.) but much of the work we did is applicable here.
So, what you have here is DBH, or Diameter at Breast Height, which, lucky for you, happens to be the most common method for estimating the biomasses of trees.  Here is the way that it works.  Basically, a research team will go out and measure the diameter of a bunch of trees.  Then they will cut down those trees and weigh them.  What they will end up with is a graph with a bunch of points that give you the weight of trees of particular diameters.  Then you fit a curve to this graph and, next time you want to estimate the biomass of a tree, you plug that tree's diameter into the equation for your curve.  There are a bunch of databases containing allometric equations for different tree species.  You just need to find one that contains the trees that you are interested in.  Given that you are working in New York, this might have what you need:
https://www.fs.fed.us/psw/publications/documents/psw_gtr253/psw_gtr_253.pdf
Though you are better off figuring out the species of the trees you are looking at and seeking out allometric equations for those specifically.  There might even be allometric information included with the data you are being provided.  One thing that may be an issue is that correlations between DBH and biomass are much more common than correlations between DBH and height.  Though both exist, you may have more trouble tracking down the latter for specific cases.  Additionally, these numbers are very rough estimates that vary a great deal depending on the techniques used to collect the data, fit the curve, and extract the equation.  In my own research, I found that log-transformed linear regression tended to be more successful over all (oddly enough) but that nonlinear regression was more effective on young forests dominated by stands of small trees.  We also had a rather odd finding that log-transformed linear regression of two lines with a breakpoint tended to be less accurate in both situations but more accurate overall (i.e. it did better on big trees than nonlinear regression and better on small trees than linear regression) but we weren't able to come up with a mechanism to explain why this would be the case so we scrapped the findings.  At any rate, all of this should illustrate that these numbers are very rough estimates that can be heavily influenced by environmental biases and that different research teams may even disagree on the proper allometric equations to use on a given species.  This is why databases are helpful, as they tend to average out a large number of allometric studies rather than relying on a single one, but even these should be taken with something of a grain of salt.
If you are expected to actually come up with these equations yourself, then you need to actually measure the diameter and heights of a bunch of trees, plot them, and fit a curve to them.  But from the sounds of it, you are only expected to estimate tree height based on diameter.  If that is the problem you are being asked to solve, chances are that there are allometric equations available to help solve it, perhaps even ones that were provided to you.

not only do you need to find a set of equations for your species, but these numbers very certainly vary between growth regions (and likely even at smaller scales). The equation(s) by Jenkins et al is an example of an attempt to get around this to a degree. The question, though, is: do you want to do your study, or do you want to do it well. @Jeremiah you're right that this is a common approach, but it has slowly fallen out of favor as we have developed more accurate (though more expensive) methods.

If a best-fit-model approach is being utilized, I would suggest that the models you've mentioned are all too constrained and will very likely not capture all of the (realistic) variation. Sometimes that's ok -- again, this is why I asked the OP for his/her end goal. If this model approach is used, however, I'd suggest building stronger models using mixed effects modelling or various nonparametric approaches. If the solution is a simple one (as in using a log curve), in this case, it almost certainly can be improved upon....

@theforestecologist I am aware of this.  My own work in this area, specifically, involved the use of differential evolution, genetic, and particle swarm algorithms to improve on these sorts of models.  But this is clearly not the sort of thing that one would be responsible pointing the questioner to.  He doesn't know what allometry is and started the question by apologizing for his lack of knowledge of the subject.  In this situation, one needs to start with the basics.  In this case, that means learning what an allometric equation is and how best-fit models work. He didn't ask for a better

way to estimate tree height.  He said that he had DBH and wanted to know if there were databases or anything he could use to estimate height with that.  There are hundreds of them and if  he had any business coming up with better models he would have already known that.  The questioner didn’t leave his level of knowledge of this subject ambiguous.  He was quite clear about it.  If someone in a bio 101 class asked you how metabolic rate scales with size, would you start going on about computer-aided modelling solutions that can more accurately

account for non-size related variability, or simply explain the mathematical relationship between surface area and volume to them?  You have to start somewhere and the questioner made it quite clear they are at the start line.  A useful answer should meet him there.

just fyi I'm not criticizing your answer, and I appreciate that you addressed the basics of allometry. The purpose of my comments are to provide a clear warning associated with this question/answer so that the OP and any future folks that put eyes on it know things are not so simple. The OP, specifically, might be asking a simple question that can be given an introductory answer, but the motive behind the question is still not clear -- it's always possible they're looking for a basic answer when they don't know that it'll be inadequate. Again, why I asked the OP what their goal was.

@theforestecologist I apologize if I came off as defensive.  That was not my intention.  In my experience, the best way to learn is to play around with new techniques, run up against scenarios where those techniques don't work, and then look into ways to improve them, learning new skills along the way.  A pet peeve of mine is when scientists attempt to dissuade interested parties from doing this because they don't have access to university resources.  The only actual concrete suggestion you provided was LIDAR.  If the OP had access to that sort of tech, they would be asking their research

advisor or company supervisor this question, not the stack exchange.  The same actually goes for anyone else who comes here looking for answers to this particular question.  It is, by its very nature, an intro level question.  They wouldn't be asking it if they were in an academic position where they had access to something like LIDAR.  When someone suggests that the only way to begin looking into a problem is if you have a funding source and a lab, that doesn't help them.  It just drives curious parties away.


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Remove the baby from the womb
Is it possible to remove the baby from the womb of a mother to cure the baby of a tumor and putting it back in the womb to be delivered naturally (the baby is 6 months)

Welcome to Biology S.E.! Can you clarify where the tumor on the baby is? Fetal surgery is definitely a thing; however, I would tend to think that a doctor wouldn't want to operate if it weren't a threat to the baby's life. If you have any questions about what kind of questions you should ask or how to ask them, please feel free to visit the Help Center, here https://biology.stackexchange.com/help.

I would think it would be nearly impossible to remove the fetus from the womb, as it is connected to the placenta, and thus to the mother.  While I'm not a surgeon, I would think using minimally-invasive techniques would give a greater chance of success. See e.g. the Wikipedia article on fetal surgery https://en.wikipedia.org/wiki/Fetal_surgery or any other of the ~3.7 million hits on "surgery "in utero"".


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Where does mycelium growing in wood get oxygen?
As per title, where does mycelium, growing in wood, get its oxygen? I mean when the mycelium is spreading into wood, say an old log, beneath the surface.
As an example, say I put mushroom dowels into a log, and seal it over with wax - standard way of doing it. Where is the sealed off mycelium getting it's oxygen ?

Hi Jimmy. What attempts to answer this question have you already taken? We ask that all question posters here attempt to search for an answer to their own question and explicitly indicate what research they've already done, what they learned, and what is still confusing or unknown to them. Our goal is not to simply be an answer site, but rather a site that promotes self-learning with some expert help along the way :). Please take a moment to edit your post with this additional detail, and it will likely be received more positively by out community. Thanks!

Thanks, yeah fair enough. I didn't really know where to start on this question, I did some googling but didn't find anything. This stack exchange question turns up on the first page of google search so I think maybe not many people have discussed this point online.

they need an aerobic environment, they absorb oxygen from water or from there air. mycelium are cells and have a cytoplasmic membrane, which can absorb oxygen the same as other eukariotes.


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How can sodium and potassium from burned organic matter (ashes) reenter the ecosystem?
If you thoroughly burn something you end up with bunch of oxides and hydroxides, as far as I know.
Sodium and potassium hydroxides are plentiful in ashes, which is why lye was created by soaking ashes in water. Lye is not exactly nice to organisms.
So the question is, how can caustic lye ever reenter the ecosystem as potassium. If it cannot, does that mean that nature cannot renew it's potassium content?

Wood ash is commonly used as a fertilizer. It acts this way in natural burning ecosystems also, where the ash from burned plants fertilizes the growth of new plants and those that survive the wildfires.
The primary constituents of wood ash are calcium and potassium salts. Lye is extracted from these salts by extracting them in water; the hydroxide salts are more soluble so the other salts are left in lower concentration than the original ash.
However, when in solution, KOH isn't really a thing anymore: you just have potassium and hydroxide ions floating around separately. Nothing special needs to be done to separate the potassium from the hydroxide ion except dissolving in water. Neutralizing the solution is then just a matter of adding an acid. There are plenty of sources of acid in soil, and rain itself tends to bring acidity. One of the sources of acidity in rain is, in fact, from fires. It is not as strong as the 'acid rain' caused by industrial sources, but there is no magic in fire that causes basic chemicals to be left behind without producing acid ones elsewhere.
The main damaging effects of wood ash are if it is applied in high concentrations where it can directly enter water sources (see for example UGA extension). In this case, it can raise pH enough to be damaging to life. Large quantities from large fires can also raise pH substantially in streams and such (see for example Burton, C. A., Hoefen, T. M., Plumlee, G. S., Baumberger, K. L., Backlin, A. R., Gallegos, E., & Fisher, R. N. (2016). Trace elements in stormflow, ash, and burned soil following the 2009 Station Fire in Southern California. PloS one, 11(5), e0153372.).
Eventually, however, there are enough sources of acid in the environment that there is no way the salts are permanently alkaline from the perspective of the whole environment.


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Analysis of dynamic connectome data?
I have heard about existence of full brain connectome data of some worms or fishes. I have heard about GEVI - genetically engineered voltage indicators - that allow to see voltage data at subcellular level. My question is: are there available the mentioned data in processed form (approriate for simulation, mathematical analysis, modelling) and, possibly, are there available some analysis and modelling of them? I am searching materials for neural code that is used in brains and those data and analysis would be very helpful for me.
I am aware of enormous body of coarse resolution MRI imaging data. But my question specifically targets connectome/neuron/subneuron level full data and their analysis.

C. Elegans is the only species with a fully characterized connectome and I don't believe there's been much electrophysiological work done on them. The GEVIs are still being optimized and have their own share of issues particularly with signal resolution - distinguishing between subthreshold changes in membrane potential vs action potential. See the embedded paper. If anything, it will be awhile before the response properties of the neurons in C. elegans are characterized. However, I'm sure you could try modeling smaller circuits where the connectivity and neural properties of the neurons are known.

Actually, there seems to be quite a bit of data on C. Elegans. IIRC recently some spiking activity was detected, while earlier it was believed there's none.


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When does DNA replicate actually?
I read on Wikipedia that when the cell enters prophase during mitosis , the DNA has already been duplicated , that is the DNA is replicated in the chromatin form , but here I see the picture which shows the already condensed DNA ( now chromosome ) divide into sister chromatids. When does DNA divide actually ?link to wikipedia -https://en.wikipedia.org/wiki/Prophase

Wikipedia is an iffy source to use. Points for adding illustrations though! Can you add link(s) so that anyone who wants to can go and read the articles themselves? If you have any questions or concerns about my thoughts on your answer, please visit the Help Center here https://biology.stackexchange.com/help

added the link.

Thank you! Are you able to reference something that isn't from Wikipedia. This article there looks pretty reputable and such; however, sometimes there is some "shady" stuff there, if you find something else, please feel free to link that here as well.

I can refer my textbook , but I would be thankful if my question is answered , I have stated my confusion quite clearly and I believe  I can get answers too.

My mistake... I thought you were answering a question not asking one. I totally misread, my apologies, your question is fine. I hope you have a great day! :)

According to This paper and most biology textbooks, S-phase or synthesis phase is literally defined by the beginning and ending of DNA replication.  The first picture does not accurately represent the nature of DNA replication and is instead a model to help people track DNA copies during stages of cell division.  DNA is replicated as chromatin and condenses to "double" chromosome form.  You can see some micrographs of DNA condensation in this paper.  You'll see that they don't condense as single chromatids, but they are already replicated.

That's exactly what should happen , It was constantly bugging me that how could the condensed DNA divide , it should be topologically difficult with all that packaging business , so they should divide in the loose form only , am I right in thinking like this ?

Yes, you're correct.  I'm not aware of any circumstances in which condensed DNA can replicate.  The first image from the textbook is meant to help student track copies of DNA through the cell cycle, but it does not represent the actual mechanics of chromosome formation.


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Is this bedbug or book louse?

Hello everyone.
I have been seeing tiny critters like this one in bed and I started to worryif they are bed bugs. Although they seem different in appearance as well as the fact that they don't seem to bite, I wanted to be sure.
Sorry if the pic is a bit hazy, they are only about 1mm long.
I also did have a bit of a humidity issue since the roof was leaky.
Does anyone know how to get rid of them. I tried different insecticides around the bed and on wooden part of the bed but nothing works.
Could they have settled in my new mattress? :(

this is almost certainly a book louse (aka a psocid). Definitively not a bed bug. See Insect identification - Is this a bedbug?

The pictures aren't very clear, but I would put this down as a book louse, not a bed bug nymph, as the body is quite elongated, which is atypical of the bed bugs and more typical of book lice.
Book louse:

Bed bug:

Courtesy of  bedbugger.com.
Check out also this page from the University of Minnesota Extension; the picture nicely matches the photo you posted in body shape.

Not book louse.

Yes the OP's specimen is most likely a book louse. @totaredom, I agree with your post. As a side note: your source is not very reliable, and I would suggest avoiding its strict usage for support for an answer. Many more reputable resources exist that could more adequately corroborate your answer.

@theforestecologist Yeah, thanks for pointing out.  Was in a bit of a hurry, I'll admit.

Great update with a reputable source. Thanks. +1

@Muze then what is it by you? Bed bug?


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Any Ideas what this insect might be?
A year ago my family and I were in Tanzania on vacation. Upon returning to our home in Alaska my wife found a small stowaway in her luggage. Feeling sorry for the poor creature we put it in a container, gave it some green leafy things to eat, some water and some paper towels pieces to hide/burrow under - thinking that its life span would be a few days/weeks and short of flying back to Tanzania this was the best we could do.
Skip ahead a year and he/she is still with us... every few days we change its food, change its bedding, and make sure it has something moist to get water from. We even took it on vacation this year to Florida and back because trying to explain how and why to take care of our friend to a neighborhood kid may work for pet cats or hamsters but we were afraid Mr. Bug might not survive.
Since we are coming up an a full year of bug sitting we are wondering what is it ? And should my daughter plan on taking it to college with her when she leaves in 6 years ?

Given how long you've had the critter, and looking at the photo, I think you have a beetle larva here; you may be "sitting" for some years yet (once you see it pupate there will be less than a year [I think] left, and the resulting adult will be much easier to identify ... if it gets that far you may want to follow up with more pictures).

FYI: please do not travel with insects. This is how nonnative species get spread -_-

I agree with Arthur. It is a beetle larva. I don't agree with forestecolgist. Most non-native species spread as unintended hitchhikers in commercial shipping, or as intentional introductions.

Topview and bottom view photo would be appreciated

@Karl I wasn't trying to suggest that personal luggage was the (i.e., the primary) way that invasives are spread -- Just one such way that it can happen. So no one should willingly and knowingly enable it to happen.

Could you please add the length of your pet?


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Does cataract condition cause red film when sun is shining?
Since two years ago I have a red film in my field of vision when the sunlight (or a white spot) is at the border (or even lightly behind) of the vision field, the red color is especially obvious at the shadows or dark places (it seems logical that the film color is more visible where there is less light).
My eye doctor recently diagnosed a little bit opalescence of my eyes, that is, a beginning cataract.
So my question is simple : does cataract condition cause a red film when sun is shining at the vision field border ?
I have an explanation for this : at the eye border the white sun light goes trough the skin and is colored red by the blood, then because of opalescence the red light propagates into the whole vision field, thus creating a red film. So if this explanation is correct then any people with a cataract condition should see a red film in such situation, that is what I want to check. Should be quite simple.
(Without strong spots there is still a mild gray film, making black appearing grayish and making shades differences less obvious to see than before this condition. Vision tests on green or red background doesn't make any differences)

"Should be quite simple." What research have you done to try to answer this question? Have you read about cataracts and 'redness of vision"? FWIW, most early cataracts are completely asymptomatic. Almost everyone gets them as they age.

@anongoodnurse I find no info about relation of vision redness with sun and cataract, so it seems that it has nothing to do with cataract, but I want to be sure of this. And this "should be quite simple" to check as I have a very early cataract, so anyone with a cataract, even with very early one, should be in the same situation as me.

Exactly! You have answered your own question. Millions of people have early (and asymptomatic) cataracts (myself included) and this is not a reported resultant effect.


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

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

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

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

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

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

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


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can you tell me what kind of animal this is?

I found this skull over 2 years ago and i have been unable to find another like it or even come across someone who knows what it is. i live in south mississippi and the animal it came from looked like a deer, or even a dog, it was almost completely decomposed. I have been curious for 2 years now and have posted this before on other sites with no luck. someone help please .

Looks rather like a boar skull, which would make sense in Mississippi (especially Southern Mississippi), where their population has been growing for decades.


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What happens to Bacteria at a low pH?
I am conducting an experiment on how different pH levels effect the growth of E.coli. After researching, it is predicted that the most acidic pH level (pH 2) will be most effective at killing (or at least slowing down the growth) of bacteria. But my question is what does pH actually do to the bacteria cell and the biology behind it. How does the pH actually affect the E. coli cell itself? Thanks for your time.

pH affects the structure of all macromolecules that compose bacteria, and indeed all cells.
Here's a shortlist of examples:
Lipids
Lipids are hydrolyzed by extreme pH levels. They undergo chemical reactions and fall apart into constituent molecules, which may be toxic. The membrane is made of lipids; if it is disrupted, the cell ceases to exist.
Nucleic acids
At low pH, RNA and DNA hydrolyze - bonds are broken between individual bases (phosphodiester bonds) and nitrogen bases break off from the (deoxy)ribose groups. Structures and hydrogen bonding (necessary for DNA replication or transcription of genes) are impaired.
In alkaline conditions, DNA typically denatures but remains intact. Structures and hybrogen bonding are still strongly impaired though.
Protein
Low or high pH environments affect ionization of amino-acid functional group ionization. This affects hydrogen bonding in such a way as to denature the molecule, because it adopts very different conformations. This of course renders the protein or enzyme non-functional, and may cause it to aggregate or become cytotoxic. If any one of the hundreds of essential enzymes fails to function correctly, a bacterium will die.
Potentials across membranes
Changes in pH have drastic effects on proton concentrations both in and outside the bacterium. Respiration depends on a concentration gradient of protons. Low or high pH will make it difficult for cells to establish a potential (different in concentration across a membrane). This gradient must be upkept for a bacterium like E.coli to generate energy, and it's difficult if protons are being neutralized or are in sheer excess!
Any one of these is enough to have a bactericidal or bacteriostatic effect! This is also why cells that do live in slightly alkaline or acidic environments have to specialize, and they have narrow windows of pH that they can survive under, because they have to compensate so much to counteract the protonation or lack-thereof in their environments.

Thank you so much! I really appreciate your help!


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'Terminal' and 'lateral' apical buds. Monopodial and sympodial branching
Macroscopically, it seems to me that the difference between 'lateral' apical buds and 'terminal' apical buds and monopodial and sympodial branching is often rather superficial, if not random. Therefore I'm suprised that such things are sometimes used in identification keys (since in some shrubs and trees, there are no apical buds at all). Does anyone know if in Biology, there is an objective definition of those phenomena, e.g. based on inner workings of a plant or microscopy?


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Is there a data base, tool or method I can use to find out which of my genes code for cytokine receptors?
I have a list of over 600 differentially expressed genes from my single cell RNA seq data analyses. I want to proceed to find out which of my genes code for cytokine receptors so that I can show on a heat map how their expression varies across clusters. Can any one give me a hint on which tool or method I can use to find out which of my genes code for cytokine receptors?
Thanks in advance.

So you're saying you want to convert the gene IDs to gene symbols such as IL15RA? R script typically works

As pointed out by @CKM, this is a simple case of finding the gene name corresponding to the ids used in the sequencing analysis. It's quite straightforward if you have a table of gene ids and corresponding names. You can do it manually for a small set of genes or use a simple script in your favorite programming language for parsing the names.

I'm sure there are many ways to go about this (including literature research via PubMed), but for a start, I searched the GO term data base which, for the search term "cytokine receptor activity" returned this, which includes a number of genes which I can download as an excel file and match them with my gene set using R.

You stole this answer from someone who answered you on Biostars.  https://www.biostars.org/p/365294/  Are you going to give yourself the best answer points now?

@swbarnes2: I asked the question on both fora and I want to share what I learned from another forum on this forum. This is because the answers I got on this forum did not directly meet my needs but I do appreciate the responses I got here. Is it a crime? By the way I slightly modified the response suggested to suit my needs.


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How do transgenic transformations cause off-target phenotypes?
I read that transgene insertions can cause off-target mutations that result in a phenotype being overly ascribed to the transgene, e.g. the increase of lifespan being ascribed to Sir2 overexpression (Burnett et al, 2011, https://www.ncbi.nlm.nih.gov/pubmed/21938067). In that particular study, they outcrossed the transgenic strain several times with wild-type to remove these off-target effects, a mutation in Dyf2 being named in particular.
I have a poor background in genetics, so I don't really understand how transgene insertions can cause off-target mutations, nor how outcrossing can isolate the intended mutation.

Could you give a link to the Pubmed page of the paper you mention?

Depends on how the transgene was inserted. Transposon and retrovirus mediated methods cause random insertions in the genome and can disrupt other functional parts of the genome. If you provide the link to the paper then it would be easier to figure out what the exact reason was.

Edited to include link

The C.elegans used in the study you linked was originally made by Tissenbaum & Guarente using the gamma irradiation protocol.
In short, the protocol provides the injection of the desired DNA construct in the worm's gonad followed by gamma irradiation of the worms.
Upon radiation exposition, the genomic DNA of the worm will break at random sites and will undergo repairing by the appropriate cellular enzymes, during the latter stage the exogenous DNA can be integrated (ligated) into the genome. However, the genomic DNA can also acquire random mutations due to the radiation. This is how transgene insertions can cause off-target mutations in this case.
With other organisms or cells, the protocols are different. To engineer mammalian cells, for example, radiations are never used but still, you have to generate breaks in the genome to edit it. Depending on the method the "off-target rate" of a given experiment may vary, but it is never zero (not yet).

When you cross a mutant organism with a wildtype one (backcrossing), in each offspring half of the alleles originate from the mutant parent and half from the wildtype.  Another way to look at this is to say that approximately half the offspring will contain any given mutation, assuming it is heterozygous in the mutant organism, and doesn't cause a fitness differential.
Because of this, on average, each time you backcross to the wildtype you lose half the mutations.  The probability of a mutation remaining after several rounds of backcrossing reduces very quickly (0.5 after one generation, 0.25 after 2, 0.125 after 3, 0.0625 after 4, 0.03125 after 5 etc).
At each round of backcrossing you test offspring and select the ones that have the intended mutation and use these for the next round, so while the probability of keeping the intended mutation stays high (~1.0) the probability of keeping unintended mutations decreases very rapidly.  This all assumes that the offtarget mutations are on different chromosomes, or far enough away from the intended mutation (unlinked) that they segregate separately and are not carried forward into the backcross generations by 'linkage drag'.

Edited to replace 'plant' with 'organism', and mention fitness differential


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Hardy Weinberg Clarification
So I am taking an introductory Biology Course and I was recently introduced to the idea of Hardy Weinberg Equilibrium. I wanted to find out why exactly we calculate the frequencies of alleles in the next population using the law of multiplication.
For example,
In a hypothetical population of let's say 300 civets, 20% of the gene pool codes for blue eye color and the remaining 80% codes for black eye color. It is given that blue eye color is recessive.
300 civets = 600 alleles total
80% code for black eye color = 480 alleles
 20% code for blue eye color = 120 alleles
When we calculate the frequencies of the next population we basically say what is the probability a given offspring will this pair of alleles. Following the example above, I would argue that the probability an offspring has two blue eye color alleles is (120/600) * (119/600). However, my textbook says that it is (120/600) * (120/600) = 0.04 but doesn't that assume replacement of alleles! My only rationale is that as the population tends towards infinity the difference becomes negligible.
Am I right?

What do you mean by "replacement of alleles"? I posted an answer guessing what you meant. If I misunderstood could you elaborate on what you mean by it and why you think it is not possible?

the population tends towards infinity

Well yes, Hardy–Weinberg principle is based on several assumptions one of them being "population size is very(infinitely) large". Another being "Mating is random".
However, even if the population is small your version of calculation does not make much sense biologically.
If we talk about civets (gonochorists) the probability an offspring has two blue eye color alleles is
(probability mother gives him blue eye allele copy)*(probability father gives him blue eye allele copy).
The two probabilities are not connected. What allele individual gets from mother has no influence over which allele they get from father. This is assured by "Mating is random" assumption.
To calculate the probability we should calculate:
(allele proportion in all possible mothers)*(allele proportion in all possible fathers)
In your example there is no information about sex of individuals, so the best approximation we have for allele proportion in females/males is the overall allele proportion in the whole population (20%) therefore the best calculation is 20%*20% = 0.04

but doesn't that assume replacement of alleles!

It seems you think that there is some rule that each parent allele copy is used only once in next generation. This is not true. Under random mating some parents can produce many children and some have none. Some allele copies get replicated several times some don't get replicated at all. In large populations the resulting random changes to allele frequency even out. In small populations allele frequency drifts.


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Inequality factor for similarity sensitive diversity
In a research article, Lou Jost has introduced the concept of inequality factor. The paper is "The relation between evenness and diversity", published in 2010.  Inequality factor allows an intuitive interpretation of the slope of a diversity profile. It corresponds to "the number of maximally uneven communities" is very intuitive.
I could not find the analogue of inequality factors in context of similarity sensitive diversity, for instance, Leinster-Cobbold diversity. Is there any equivalent notion of inequality factor for the similarity sensitive case? Could anyone suggest me some readings?


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Why is a urea solution hypotonic relative to RBC?
If I place a RBC in 0.5M urea we see haemolysis.
My textbook says that "the solution is hypotonic. Urea enters the RBC down it's concentration gradient. Water follows the movement of urea by osmosis. This influx of water causes lysis".
I am very confused by this, for a number of reasons.

I thought tonicity only applies to non-penetrating solutes (i.e. a solution is hypertonic relative to a cell if the solution has a greater concentration of non-penetrating solutes then the intracellular fluid). If urea can penetrate the membrane, then why is the solution hypotonic? As a penetrating solute isn't it not factored into tonicity.
If urea is a penetrating solute, then won't it just come to an equilibrium across the cell membrane, and hence there will be no net osmosis since the concentration inside the cell will the same as that outside the cell.

I feel like I have a conceptual failing here, but the more I google the more confused I get.

It would be helpful if you could quote the entire scenario from your text book.

I think you have the conceptual understanding down, but my guess is that the textbook is not representing the situation quite correctly.  Based on the phrasing of the statement, I can imagine they are describing one of two situations:

Imagine a dropping a cell in to a solution of 0.5 M urea with no other solutes.  Urea will diffuse across RBC membranes due to facilitated diffusion.  It won't really factor in to this situation much.  So, the RBC contains proteins and other solutes that cause water to flow in to the cell and the cell lyses.  I don't think this is what the textbook means.
Now, imagine a situation in which you precisely calculated the water potential of a RBC.  You mixed up an isotonic solution of urea and some non-penetrating solutes.  This solution is perfectly isotonic at first, but as the urea diffuses in to the cell, it alters the water potential of the cell and the outer solution leading to osmosis.  I think this is the situation the textbook is trying to describe.

Imagine a third situation now in which a RBC is at equilibrium with a solution.  If you just added urea to the solution, it would not affect osmolarity in the long term for the reason you describe.


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Insect ID, Ecuador
Picture was taken in the Ecuadorian Amazon in January 2019, during the day, elevation about 300 meters. The size was not recorded but might be no bigger than a housefly judging from the photo. It appears to be a leafhopper of subfamily Gyponinae. Any additional info on the genus or species would be appreciated.

I am no entomologist, but that looks like it may be a type of cicada. Is it one of these perhaps?

Hi, terdon. Thanks for the comment. The bug was quite small, and does look like a cicada, but a very small one. From some info I received, I think this might be a leafhopper. Leafhoppers are relatives of cicadas.

Please [edit] your question and add the size since that will likely help identify it. Also tell us what kind of environment you found it in (jungle, yes, but was it in the canopy? On a tree bark? On the forest floor? Did it have a nest you could see?) The more details you give, the likelier it is someone will be able to identify it.

Well, it was taken about a month ago, along with about 600 other subjects, so what I know about it is pretty well in the photo. It was on a leaf. It was small compared to the leaf, although I don't have a record of the size of the leaf. I'm satisfied that it is a kind of leafhopper, subfamily Gyponinae. That is a varied group, but that is fine for now.

Please [edit] your question and include these details. Comments are easy to miss, hard to read and can be deleted without warning. You want the next person to read your question (who might actually know what they're talking about and not just be stabbing in the dark like I am) to have all the details easily accessible.


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What's a reasonable time constant for a mathematical model of a neuron?
Background
I've been studying various mathematical models of neurons. So far I've covered the classic Hodgkin-Huxley model (to describe the potential difference of a single neuron) and the integrate and fire model for two neurons (to describe the voltages of interacting neurons). I am now studying a firing-rate model which describes the firing rate of neurons, not their voltage.
All of these models include a time constant $\tau$. For the Hodgkin-Huxley and integrate-and-fire models $\tau$ tells us how fast the channels and pumps open/close in response to an action potential.
I am currently working with a two-neuron system of one excitatory neuron and one inhibitory neuron. It is described by the equations
$\tau_E \frac{dV}{dt} = f(v_E, v_I, \theta)$
$\tau_I \frac{dV}{dt} = g(v_E, v_I, \theta)$
where

$v_E$ is the firing rate of the excitatory neuron
$v_I$ is the firing rate of the inhibitory neuron
$\theta$ is a set of constant parameters.
$f$ and $g$ are linear WRT $v_E$ and $v_I$

I have fixed all parameters $\tau_E$ and $\theta$ leaving only $\tau_I$ to be varied. Certain values of $\tau_I$ cause stability while others cause instability.
For the parameters $\theta$ that I'm using I have found that disregarding the possibilities of $\tau_I<8$ and $\tau_I>791$ greatly simplifies the analysis (because of the way the eigenvalues of the Jacobian matrix work out). I also have reason to believe that it might be alright to disregard these values.
All of the $\tau$ time constants in all the examples I've seen so far have been around $10ms$.
Question
$791$ seems very high, but is it so biologically unreasonable that it can be completely ignored? What's to stop one neuron being $1000$ times more responsive than another one given there's such diversity in neuronal structure and function over all types of neurons? Are there examples of this?
$8$ seems completely reasonable for a time constant. Surely values under $8$ can't be disregarded completely?

How these parameters relate to your firing rates? Neurons have a maximum firing rate of 500-1000 Hz.


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Is oxygen's paramagnetism biologically relevant?
It seems our most common everyday O2 molecule happens to be a paramagnetic one (see https://en.wikipedia.org/wiki/Oxygen).
But, does this have a biological relevance as well? In other words, Do any chemical processes occurring within the physical volume of any entity considered "living" depend in any way, shape, or form on oxygen's paramagnetic properties?
(It seems to me the answer would be "no", but I am no expert in this field!)

This Q is too broad.

Biology isn't a very narrow field  either ; ) Would the following phrasing be any more specific: Do any chemical processes occuring within the physical volume of any entiy considered "living" depend in any way, shape, or form on oxygen's paramagnetic properties?

The answer is either yes or no; I don't think this is too broad.

The answer to your re-phrased question

"Do any chemical processes occurring within the physical volume of any entiy considered "living" depend in any way, shape, or form on oxygen's paramagnetic properties?

is an emphatic 'yes', and this answer may be substantiated with a single word: haemoglobin.
Pauling and Coryell discovered in 1936 that the oxygen in both oxy-haemoglobin and CO-haemoglobin is diamagnetic, and I quote from the last paragraph of that great paper:

It is shown by magnetic measurements that oxyhemoglobin and carbon-monoxyhemoglobin contain no unpaired electrons; the oxygen molecule, with two unpaired electrons in the free state, accordingly undergoes a profound change in electronic structure on attachment to hemoglobin.

This result has 'stood the test of time' and is a key observation in explaining at a  molecular level the allosteric and cooperative properties of haemoglobin.  IMO, it is one of Pauling's great observations, and illustrates his phenomenal powers of deduction.
As Pauling points out, Faraday also investigated the magnetic properties of haemoglobin and recorded in his notebook 'Must try recent fluid blood'.
To again quote Pauling and Coryell :

If he had determined the magnetic susceptibilities of arterial and venous blood, he would have found them to differ by a large amount (as much as twenty per cent for completely oxygenated and completely deoxygenated blood); this discovery without doubt would have excited much interest and would have influenced appreciably the course of research on blood and hemoglobin

Magnetic properties usually do not play a significant role in chemical reaction unless some external magnetic field is applied. The magnetic properties are resultant of the chemical properties and it is the chemical properties that really matter. And how would the biochemistry of oxygen transport be affected because of the magnetic properties of oxygen? The only biological process that I am aware of that is driven by magnetism is magnetotaxis and it involves the ferromagnetic substance magnetite.

I got your point but I was arguing that the paramagnetism of dioxygen per se does not play any role in any of its biochemical reactions. The chemical properties that cause paramagnetism also affect some of the reactions of dioxygen. So even if those two properties are correlated there is no cause-effect relationship between them. See my answer.

It sounds a bit like chem exam question to be honest... Or at least the answer does... namely that O2 being paramagnetic creates a "spin barrier" that prevents most organic compounds from reacting fast with atmospheric oxygen:

The magnetic properties of O2 are not just a laboratory curiosity; they are absolutely crucial to the existence of life. Because Earth’s atmosphere contains 20% oxygen, all organic compounds, including those that compose our body tissues, should react rapidly with air to form H2O, CO2, and N2 in an exothermic reaction. Fortunately for us, however, this reaction is very, very slow. The reason for the unexpected stability of organic compounds in an oxygen atmosphere is that virtually all organic compounds, as well as H2O, CO2, and N2, have only paired electrons, whereas oxygen has two unpaired electrons. Thus the reaction of O2 with organic compounds to give H2O, CO2, and N2 would require that at least one of the electrons on O2 change its spin during the reaction. This would require a large input of energy, an obstacle that chemists call a spin barrier.

(quote from McQuarrie and Simon's (free) textbook Physical Chemistry: A Molecular Approach).

And by the way, there also exists a variety of singlet oxygen (1Σ -- second excited state) that is not paramagnetic, but is fairly unstable a room temperature.

Interesting, so not exactly out of some kind of interaction with magnetic fields of any sort (which is what I usually think of regarding paramagnetism), but rather due to the quantum effects (such as this "spin barrier") that just also happen to give rise to "paramagnetism" as well. It seems the answer would then be "no", although the underlying causes of paramagnetism do give rise to other more "useful" properties (such as inhibitions of chemical reactivity) however.

@ManRow you are right. Unless there is an interaction with the applied magnetic field, the magnetic properties per se do not have any effect on the chemical reactions.

According to my reasoning, the answer is no.

Bulk magnetic properties are a resultant of the atomic/molecular (chemical) properties and chemical reactions are usually not dependent on the magnetic properties per se. Magnetic properties can have a role if:

There is an externally applied magnetic field (https://chemistry.stackexchange.com/q/24507/5295). Magnetotaxis in some bacteria involves signalling by microcrystals of magnetite and greigite that guide the bacterial locomotion in response to the geo-magnetic field.
Some of the reactants or the components of the reaction center exert magnetic field (ferromagnetic materials, for example).  Herve et al (1984) showed that incorporation of magnetite particles increased the yield of some intermediates (light absorbing transients) during the photoreduction of benzophenone.

In any case I haven't come across any research that states that the paramagenetism of molecular oxygen is a factor in any biochemical reaction. As pointed out in the other answer, the stable triplet state of dioxygen is slightly less reactive compared to the singlet state. The paramagnetism that results because of the triplet state is not the cause of the lower reactivity. In other words, there is no cause and effect relationship.


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Regulation of LBD33 genes Arabidopsis. If LBD 33 gene is up-regulated by auxin then why does expression decrease when increasing auxin concentration?
I have a question regarding the regulation of lateral boundary domain genes in Arabidopsis (specifically LBD33). I am an undergraduate student trying to understand the results of a lab where I measure the regulation of gene activity by using GUS staining technique. I have included a photo of images taken of Arabidopsis under different treatments:

A) Wild type no auxin, the wild type has no GUS gene inserted thus no transcription of genes that code for GUS. This was our negative control.
B) Positive control CyclinB1 where the promoter has been fused upstream of the coding sequence for GUS. GUS staining always present.
C) LBD 16 mutant no auxin GUS promoter is fused downstream, without auxin genes GUS is not transcribed.
D) LBD 16 mutant exposed to 1um IBA, GUS staining on lateral roots.
E) LBD 16 mutant exposed to 10um IBA, even more GUS staining on lateral roots compared to D) treatment.
....So far I think I understand, below is where I am having problems interpreting my results.
F) LBD 33 mutant no auxin. staining in leaf and roots (all the literature I have found says LBD genes are only active in lateral roots but the stain is present in leaves)
In images G) LBD 33 mutant exposed to 1um IBA, and H) LBD 33 mutant exposed to 10um IBA, the expression of LBD 33 genes seems to decrease by adding more auxin, but when I read journal articles they all say that auxin up-regulates the transcription of LBD33 gene. I thought that if these genes are auxin induced shouldn't expression increase when more auxin is added?


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Prostate, seminal vesicles or testis which one is bigger(by volume and size)?
I can't understand this by looking at these photos, especially the last picture makes me more doubtful.
Do you know which of them is the biggest one by volume?

Another question is, what is the biggest organ in the male reproductive system? (Note that the bladder is not a part of it.)

Why does it matter?

@Bryan-Krause Comparing the size of male reproductive system organs

That doesn't answer the question of why it matters.

@BryanKrause  Be sure that I don't want to know this just to satisfy my curiosity, I faced with it in my multiple choice test. I don’t think it matters much what you study anyway.

I'd note that the images you've examined are representations, not specimens. Generally, don't expect everything to be to scale. I'd suggest Rohan's Color Atlas of Anatomy if you want actual specimens. There is a plate there that should help you.

@BryanKrause the relative size of anatomical structures is a reasonable question in and of itself. It's useful if, for example, you want to identify them. OP, you've asked two questions: which is bigger, the prostate or the seminal vesicle, and what's the biggest organ. You could improve this question by defining your terms (bigger how? by volume?) and by limiting it to a single question.

The average seminal vesicle length was 31±10.3mm and its average volume 7.1±5.2cc. That is verified by another source which states 6-10mm in controls.
The average prostate volume ranges from 20 to 40cc from ages 30  to 80, 3-2-3cm for younger males 5-4-5 for older ones.


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Can a hydra get cancer?
Because hydras have immune systems, telomerase activity, and Piwi-piRNA like cancer cells I wonder if they can get cancer?

Yes.

Research in cnidarians shows that even pre‐bilaterian animals can develop neoplasia (Domazet‐Lošo et al., 2014). Two different species of Hydra have presented with tumour‐bearing polyps. The cells in these tumours were invasive, which suggests that metastatic capacity has ancient roots. Additionally, the tumours had several orthologues to tumour‐related genes in mammals and displayed parallels to the hallmarks of cancer in vertebrates. The proposed mechanism for tumourigenesis in Hydra is the accumulation of stem cells if they are not appropriately removed by programmed cell death (Domazet‐Lošo et al., 2014). Scientists have also identified several cancer‐like lesions in corals (Aktipis et al., 2015).

--From humans to hydra: patterns of cancer across the tree of life

Yes. May I suggest a mention that this is a significant finding in understanding the evolutionary origin of cancer (i.e., it supports the prediction that cancer originated with the earliest animals).

@DeNovo : I'm not really sure that the (rather obvious) observation that as soon as the very first DNA (etc.) existed there was (by the very definition of what it is) then a potential for copying errors really qualifies as a "prediction"? just my (not entirely) latent pedant gene kicking in, sorry about that :)

Cancer is intrinsic to any multicellular organism with the same master genome in multiple  cells. For an organism to have a coherent structure, there must be coordination and control between the cells.  If there is genetically based control, those genes can mutate to be dysfunctional, and some versions of dysfunction will release control of the genes causing cellular replication, which will form a neoplasm if not suppressed by other cells of the organism (which may be dysfunctional).

@Pelinore the prediction is that cancer originated with the first animals, not the first DNA (and not single celled organisms, see: the bit where I address that in this answer). The current species who's lineage diverged from other animals at the earliest point (but remain animals) are basal metazoans, like the hydra. Cancer, as we understand it, is not observed, nor is it predicted to exist in single celled organisms. I can't seem to find my reference to the computational model that makes this prediction. If i can find it, i'll add it later.

@DeNovo fair enough, so it needs multi cell organisms before you can call any copy errors cancer, not really anything to do to do with what I said though, I still say "prediction" isn't really the right word.

@Pelinore cancer is more than copy errors. You might find this seminal paper interesting, if you'd like to learn more about how cancer biologists define cancer.


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Did the Broadbill Swordfish population fully recovered?
Regarding the Broadbill Swordfish Xiphias gladius:
I read Richard Ellis "Swordfish: A Biography of the Ocean Gladiator", Chicago University Press, 2013. The chapter about industrial-strength fishing described that up to the late 20th century, swordfish population was decimated due to overfishing. In chapter 11 he discusses whether the swordfish is endangered and describe the late 1990's conservation efforts. It says that there is a rise in swordfish population in the North Atlantic (but say we don't know if the population fully recovered to its heydays) and say there is little information for the Pacific and Mediterranean populations.
I found some info in https://www.fishwatch.gov for the North Atlantic and North Pacific population, saying that north Atlantic and western north Pacific are not overfished and not subject to overfishing (I think this is good), while the eastern north Pacific is not overfished but subject to overfishing. The ICCAT published a report Atlantic, ICCAT 2017 which is hard to read. What I understood the north Atlantic is not overfished while the south Atlantic population is overfished and in danger.
For the Pacific, see Pacific, ICCAT 2018, which says that the north central and western Pacific are not overfished:

Overall, the base case model indicated that the WCNPO swordfish stock is not
  likely overfished and is not likely experiencing overfishing relative to MSY-based
  or 20% of unfished spawning biomass-based reference points.

These reports are hard to read for non-expert, so I ask here few questions about the populations of swordfish:

Is the swordfish endangered species?
Is the swordfish population sustainable?
Per population P = { North Atlantic, South Atlantic, North Pacific, South Pacific, Indian, Mediterranean }:
3.1 Is the population P endangered?
3.2 Is the population is safe (non-threatened) or least concern?
3.3 Did the population fully recovered and reach a healthy size?


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Using expression vector to express arsenite oxidase genes in E. coli
So I am trying to express a gene cluster that can oxidize arsenite into arsenite autotrophically. The arsenite oxidase gene cluster sequence is linked here: https://www.ncbi.nlm.nih.gov/nuccore/AY345225.3
I originally was going to clone this gene into the pBAD-DEST49 expression vector, and transform it into E. coli C600, but the vector is out of stock, and I need it quickly. I was looking through Sigma Aldrich, and I found this vector: PSF-OXB20. I plan to clone the genes into this vector.
I do, however, need some advice. I am not 100% sure on if this vector would work, or if the genes would be overexpressed. My question is would this vector work out, or is there any better ones out there. Any advice would be appreciated, and if I need to include more details, just let me know.


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Why is exclusive breastfeeding recommended for 6 months only?
The WHO recommends exclusive breastfeeding for the first 6 months of a child's life.

Review of evidence has shown that, on a population basis, exclusive breastfeeding for 6 months is the optimal way of feeding infants. Thereafter infants should receive complementary foods with continued breastfeeding up to 2 years of age or beyond.

Their website mentions "review of evidence", but what is that evidence? Why 6 months and not 4 or 5 or 7 or 8 or 9 or anything like that?
Can anyone give which review is WHO talking about?

I guess this is the review (ISBN: 92 4 156211 0) that they are referring to.

We found no objective evidence of a “weanling’s dilemma.” Infants who
  are exclusively breastfed for 6 months experience less morbidity from
  gastrointestinal infection than those who are mixed breastfed as of 3
  or 4 months, and no deficits have been demonstrated in growth among
  infants from either developing or developed countries who are
  exclusively breastfed for 6 months. Moreover, the mothers of such
  infants have more prolonged lactational amenorrhea. Although infants
  should still be managed individually so that insufficient growth or
  other adverse outcomes are not ignored and appropriate interventions
  are provided, the available evidence demonstrates no apparent risks in
  recommending, as public health policy, exclusive breastfeeding for the
  first6 months of life in both developing and developed country
  settings. Large randomized trials are recommended in both types of
  setting to rule out small adverse effects on growth and to confirm the
  reported health benefits of exclusive breastfeeding for 6 months.

However, another report suggests that exclusive breastfeeding for a long time may lead to deficiency of some nutrients which cannot be supplemented via maternal diet.

The dual dependency on exogenous dietary sources and endogenous stores
  to meet requirements needs to be borne in mind particularly when
  assessing the adequacy of iron and zinc in human milk. Human milk,
  which is a poor source of iron and zinc, cannot be altered by maternal
  supplementation with these two nutrients. It is clear that the
  estimated iron requirements of infants cannot be met by human milk
  alone at any stage of infancy. The iron endowment at birth meets the
  iron needs of the breastfed infant in the first half of infancy,i.e. 0
  to 6 months. If an exogenous source of iron is not provided,
  exclusively breastfed infants are at risk of becoming iron deficient
  during the second half of infancy. Net zinc absorption from human milk
  falls short of zinc needs, which appear to be subsidized by prenatal
  stores.

Both these reviews are from WHO website; you can search for different WHO research materials on the site.
Note: WHO does not say that breastfeeding should not be continued till a later stage. As noted in the review, exclusive breastfeeding for more than six months can cause some nutritional deficiencies. However, reducing exclusive breastfeeding to 3-4 months can reduce the immunity of the infant.

So basically they found the optimal time for exclusive breast feeding was between 4-6 months. I wonder what reason they listed 6 instead of the range?.

@John In such studies it is difficult to make fine measurements. Perhaps they just tried with 4 & 6 and didn't check other durations.

I liked the answer, but now I really want it to change, WHO should not make vague guidelines without sufficient data.

@AnubhavGoel WHO is trying to do best with whatever data they have. Note that whatever they say is a recommendation and general guideline. It is always better to consult a doctor for specific cases.

I am a medical student myself, and the part is doctor here dont see it as guidelines but as sacred stone line.

@AnubhavGoel exactly


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Can (or have) antiviral drugs created drug-resistant viruses?
Evolution/emergence of antibiotic-resistance in bacteria is a known effect of extensive use of pharmaceutical antibiotics.
Pharmaceutical antivirals have come into extensive use in recent decades – e.g., Tamiflu for influenza; Harvoni for hepatitis C; Valtrex for herpes.  Some are even prescribed as ongoing "suppressants."
Has anything analogous to antibiotic resistance (i.e., antiviral resistance) been observed in viruses treated with pharmaceutical antivirals?  If not, are there theoretical reasons this would be unlikely (or impossible) to occur?

Resistance to antiviral therapy is a problem in the treatment of many viral illnesses.
Influenza is particularly significant given the epidemiological characteristics of the disease. This Nature Medicine article gives a good overview of oseltamivir resistant pandemic H1N1, which is a useful example, since our assumption that resistant virus would not spread very effectively was (probably predictably) not valid.
HIV is an excellent case study as well, since antiretroviral resistance is such an important issue in the treatment of that particular infection, and demonstrates the challenges of outwitting a pathogen with such a high error rate. This became apparent quite soon after introduction of (initially successful) monotherapy with AZT. In fact, preventing the emergence of resistant virus within the population of virus in a given patient is typically the primary consideration in choosing a drug regimen.
With regard to the other examples of antiviral treatment you mentioned, HCV resistance is well reviewed here. HSV resistance is reviewed here. Resistance has been observed in both examples, though it is more often considered in the normal course of treatment for HCV than HSV. I'd note that Harvoni, which you mentioned, is a combination therapy (ledipasvir-sofosbuvir). Combination therapy is one common strategy for preventing the emergence of resistance


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Which moth is this?
City name - Mohali (Chandigarh)
Season - winter(after rain of western disturbance)
Location - IISER Mohali hostel near tube light of mess
Time - 21:49, 22 February 2019
Size - 1.5cm

2:

I'll swear it's a hawk moth, which hawk moth is another matter though.

Providing geographical location is good but it need not go into details which nobody else would be aware of. For example, you should indicate in which part of the world (and country) your location is and what is the general weather/vegetation conditions in that region. Any average person (even an Indian) may not know where Mohali is. You have mentioned about the weather but you should clarify what "western disturbance" is. Now, the specific details about your institute hostel and mess are not relevant unless you have a unique ecosystem. In that case you should explain the local conditions.

It does look like a gray hawk moth "species" with hind wings folded underneath. The body shape seems right, but the size estimation seems too small.

It resembles a Laothoe species, indeed member of the hawk moth familie. However, all Laothoe sp described on Wikipedia have a wing span over 7cm and none of them occurs in India.

It's bombyx mori moth


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Difference between prions and amyloid proteins?
Amyloid and prions are misfolded proteins, but what, if any, is the difference between them?
Is amyloid a type of prion with a fibrillar structure?

Amyloids are protease resistant insoluble fibrils formed because of (mis)folding and aggregation of soluble proteins (Rambaran and Serpell, 2008, Sabate et al., 2015). The first definition of prion was given by Prusiner (1982):

Because the novel properties of the scrapie agent distinguish it from
  viruses, plasmids, and viroids, a new term "prion" is proposed to
  denote a small proteinaceous infectious particle which is resistant to
  inactivation by most procedures that modify nucleic acids.

Many prionic diseases are characterized by amyloid fibril formation and therefore some (if not many) researchers consider prions to be a subset of amyloids.

Prions are considered a subclass of amyloids in which protein
  aggregation becomes self-perpetuating and infectious.
(Sabate et al., 2015)

However, the amyloid structure formation is not essential either for the autopropagation or disease progression (Moore et al., 2014).

When wild-type C57BL/10 mice are infected intracranially with the RML
  mouse prion strain, PrPSc accumulates in diffuse nonamyloid deposits
  and brain pathology is distinguished by the hallmark gray matter
  spongiosis for which TSEs are named. Conversely, when transgenic mice
  homozygous for PrPC lacking the GPI anchor (Tg44 or “anchorless” mice)
  are infected with the same RML strain, the incubation time is longer
  and PrPSc accumulates in dense perivascular amyloid plaques with
  little or no gray matter spongiosis.9−11 Similar amyloid PrPSc
  deposition and disease resulting in death has been observed in humans
  with an aberrant stop codon in the C-terminal portion of the PrP
  sequence, resulting in the generation of PrP lacking the GPI anchoring
  group as well as some amino acid residues.13−16 Thus, GPI-anchoring of
  PrPC to the plasma membrane appears to be a primary factor determining
  the type of PrPSc deposition and the development of brain pathology.

You can say that the prion protein PrPC is amyloidogenic but it is not an amyloid.
There are non-pathogenic (and in fact useful prions) found in fungi. Many of these beneficial prions also form the amyloid (like) structure but they can be disaggregated by chaperones (Wickner et al., 2018). Now again, it is not essential for these beneficial prions to form an amyloid structure.

Prions (defined as “infectious proteins”) need not be amyloids. The
  vacuolar protease B (Prb1p) of Saccharomyces cerevisiae is made as an
  inactive precursor that is normally cleaved and so activated by the
  action of protease A (Pep4p) [32]. However, in the absence of Pep4p,
  mature active Prb1p can activate its own precursor [33]. This
  self-activation can propagate and pass from cell to cell in an
  infectious manner, acting like a prion, and named [BETA] [34]. In the
  absence of Pep4p, [BETA] is necessary for meiosis and spore formation
  and for survival in stationary phase [34]. It is thus a functional
  prion.

[SMAUG+] is another example of a non-amyloid yeast prion which has beneficial effects (Chakravarthy et al., 2019 and Itakura et al., 2019; Jarosz group). Unlike Prb1p, [SMAUG+] actually forms self-propagating aggregates.
My summary
Many known prions are amyloidogenic and can switch to amyloid form. However, as per the definition, prions are "infectious" or in other words, self-propagating proteins.
What qualifies as a prion depends on our definition. Mode of action of most known prions is catalyzing a change in the protein fold. Wickner et al (as quoted above) reason that the original definition does not explicitly include the mode of action and hence proteins that activate themselves via proteolysis should also be considered prions. Jarosz's group has shown an example of a non-amyloid prion that forms self-propagating aggregates. It quite likely that more such proteins will be discovered in near future.
In any case, "amyloid" is a structural property whereas "prion" is a functional property and they cannot be considered a sub/superset of one another, even if they happen to be correlated.
The bottomline is:
Amyloid is a form of supramolecular protein structure which is often formed by many prionic proteins. However, not all amyloid forming proteins are prionic and not all prions necessarily form amyloids.


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Double Digestion with Restriction Enzymes Using Different Buffers
I am currently working on preparing a 9 kb sequence of DNA for restriction digestion into the pBAD30 expression vector. There are very few restriction enzymes that do not have a restriction site located on my insert, and since I am using 2 restriction enzymes in my digestion, I had little choice in choosing my restriction enzymes. The only two restriction enzymes that will work for me are Xmal and KpnI. XmaI uses CutSmart buffer while KpnI uses NEB buffer. The efficiency of XmaI in CutSmart buffer is 100% while the efficiency of KpnI in CutSmart buffer is 50%. Would it be easier to perform a double digestion using CutSmart buffer and 2x KpnI than to perform two consecutive digestions?

Hi Hunter. What conclusion have you come up with yourself? You've received a close vote on your question because another user likely assumes you're looking for others to do your work for you (i.e., figure out which approach is best). I think you'll get a positive response if you can demonstrate a little more explicitly that you've thought about this on your own and that you've spent some time researching to support one way or the other. It will likely sharpen your question and create a more interesting dialogue and answer. Thanks!

I am definately not asking others to work for me. I am simply asking a scientific question that I was unable to find the answer to. I should not have to fear asking a logical scientific question. Closing this question is only holding back the scientific community and preventing others, like me, from learning more about science.

Hunter please don't get mad. I'm not even the one that voted to close. I'm just letting you know that some have interpreted your question as asking for an answer to a question you haven't fully indicated you tried answering on your own. If you were to indicate explicitly what you have already done to try to answer the question (e.g., where have you looked, what have you read, etc.), then this concern is avoided. Closing questions might be holding back some individuals, but it's encouraging most to take that extra step toward being effective scientists: self-guided learning.

(You've got to learn where else to look for answers b/c you can't always rely on Q&A websites to exist or to give you accurate (or even any) answer at all.)

@theforestecologist I apologize for sounding angry. I will do better in specifying my efforts to solve the problem in the future. Thank you for the advice.

In my opinion question seems to be in correct format (may be I am seeing edited version). @HunterRees question is more of practical than theory.He is facing problem as he is stuck at one of the steps of his experiment.In search of solution, he has explained what he has found (like combination of buffers he mentioned).However, before performing the experiment he is seeking some more advice from the experts on this.

In my experience, a double digestion in CutSmart buffer will work perfectly well. The reaction may proceed slower, but incubate it a little longer and run a gel after the digestion - you'll see whether it has worked. The other answerers unfortunately did not mention that the best way is to check the restriction products yourself on a gel. Cut out the fragment from the gel you need (and purify) if you want to avoid undigested plasmid. See if the plasmid fragment sizes correspond to the correct cutting sites. Basic lab practice and it takes very little time!
Beware of star activity - ask a technician to sequence your fragments or plasmids to be sure it's all going well (this is good lab practice), in case you see unexpected bands on your gel that may indicate unwanted restriction activity. This is not so common, though :)

I would have thought checking a restriction digest on a gel goes without saying. Also, is your experience actually using KpnI in CutSmart? NEB explicitly warns that extended digestion with this enzyme may result in star activity, though I don't know how serious of a problem it actually is.

Even with star activity, the enzyme is partially doing its job correctly and the plasmid is partially digested correctly. Running the product on the gel and purifying the correct fragment is the best way to do it for three reasons: (i) you know exactly what your product is, (ii) you don't need to purchase, wait and/or troubleshoot new enzymes, and (iii) you're fostering that sweet sweet scientist thinking, rather than being a protocol zombie - my technician's words, not mine :-) There is one quite minor downside: you can't do this with very little quantities of plasmid (does not apply here).

Fair enough. I still prefer to use the optimal buffer, which is especially easy for me since I do sequential digests. To each their own.

NEB double digest planner is suggesting to use 2.1 buffer for your combination of restriction enzymes (XmaI 50% and KpnI 75% activity). I would be more worried about the star activity of KpnI in CutSmart buffer than the lower activity. The latter can be overcomed by prolonging reaction time or using more enzyme.

If you haven’t already ordered your enzyme, you could get high fidelity KpnI, which has been engineered for use in CutSmart.
You could also consider doing a sequential digest rather than a double digest (ie digest with one enzyme in its optimal buffer then change the buffer for digestion with the second enzyme). It is more work but benefits from easier troubleshooting in case one of your enzymes is not cutting (which can occur frequently if you have a freezer full of 10 year old enzymes).


text:
How deep could a human swim with SCUBA apparatus?
Using normal SCUBA apparatus and wet suit, how much pressure can the human body withstand? This is assuming that they descend as gradually as necessary for their body to make adjustments. What would be first symptoms that they experience as they descend? And if they descend to the deepest depth that they can reach without immediate permanent harm, how long can they spend at that depth before time related symptoms set in?

It's not a question that has a simple answer.  Do you mean diving with simple compressed air?  Then 130 ft/39 m is the accepted max for recreational divers.  With different air mixes, you can go much deeper.  The other problem is not going deep, though, it's coming back up.  Gas dissolves in the blood at high pressure, and if you come up too fast makes bubbles, AKA "the bends", which can be fatal.  All this and more can be found in the Wikipedia article ttps://en.wikipedia.org/wiki/Deep_diving or through a simple search.

As far as I can find the current world record for "scuba" diving is 1,090 ft 4.5 in set in 2014.
The previous record was 1,044 ft set in 2005 so (as with most human endurance & physical achievement records nowadays) we're most likely at the limit of the possible there.
Barring a few more feet (or even just inches) of course.
Howsoever, that's only normal scuba diving equipment
Deep diving using hydrox and trimix has reached depths of 1,644 ft (1977) & 1,752 ft (1988).
So the answer depends on if you're asking about with normal commercial scuba gear using bog standard compressed air or if you want to include breathing mixes etc to help alleviate the bends.


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If bacterial plasmid DNA is methylated then how do we digest it using restriction enzyme in cloning experiments?
So, I was reading about how bacteria protects its own DNA by methylation against restriction enzyme. But if the plasmid DNA is also methylated then we can't cut plasmid using restriction enzyme for doing cloning. And if we are isolating this plasmid from Methylase deficient strain so that the plasmid is not methylated, won't it would be digested by the bacterial restriction enzyme. Do we isolate these plasmid from a strain that is also unable to produce restriction enzyme ?


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The phylogenetic definition of the clade Dinosauria
Up until two years ago the clade of Dinosauria was defined as all the descendants of the most recent common ancestor of Triceratops and birds. From Wikipedia:

Under phylogenetic nomenclature, dinosaurs are usually defined as the group consisting of the most recent common ancestor (MRCA) of Triceratops and Neornithes, and all its descendants. It has also been suggested that Dinosauria be defined with respect to the MRCA of Megalosaurus and Iguanodon, because these were two of the three genera cited by Richard Owen when he recognized the Dinosauria.

However, after the resurrection of the clade Ornithoscelida by Baron et al in 2017 (see here), as the clade consisting Ornithschia and Theropoda, the MRCA of Triceratops and birds is defining Ornithoscelida and not the whole Dinosauria, assuming we still define Sauropodomorphs as dinosaurs.
So if dinosaurs include Sauropodomorpha, Herrerasaurs, Ornithoschia and Theropoda,  what is the most updated phylogenetic definition of the clade Dinosauria?

As of right now it is still the same, the evidence for sauropodomorpha being a outgroup is not statistically more reliable, this may change, however this will still not have much impact. There are several ways in which dinosauria is defined.
The most recent common ancestor of Megalosaurus and Iguanodon is also sometimes used since they were the original animals used to define the group.
The last common ancestor of Triceratops horridus, Passer domesticus, Diplodocus carnegii, and all of its descendants is also used just because of Baron's work.
Finally there are several unambiguous synapomorphies used to define the group, including such things as ankle structure. A full list can be found here.
In a group as well known as dinosaurs, a discovery like Baron's (if it holds up) is just going to lead to a change in the definition.