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Why bacteria and viruses are so much smaller than animal cells?
Why are bacteria and viruses so much smaller than animal cells? -
I don't have more information about the question, sorry if this is too vague.

I actually think that this is an interesting question. The problem is that the format for this site would make this a difficult question to answer properly. Viruses use the cells they infect to make more copies of themselves, so right there, they would need to be much smaller than the cell itself, otherwise it couldn't reproduce itself. There are also energy efficiency issues, replication times, simpler genomes, fewer organelles, and on and on to explain bacterial smaller size.

Cells/viruses vary in size mainly according to their function, components & requirements imposed by cell division/virus replication.
Bacterial cells are so small because they need a large surface area to cell volume to take in nutrients. Bacteria accumulate nutrients from the environment by diffusion alone, and so adopt certain sizes and shapes so they can import nutrients most efficiently. other evolutionary advantages are also existent in response to the demands of the environment and predators
Viruses function is pretty minimalistic. they pretty much consists of nucleic acid surrounded by a protective coat of protein called a capsid. this is the primitive virus, all it nedds is to infect cells and pass the information stored inside them.
The size of animal cells however depends partially on the type of cell and its function. Red blood cells are pretty small in comparison to other animal cells, they don't need to divide (so do not own a nucleus) and need a large surface area in order to diffuse Oxygen efficiently. Egg cells for example serve to store nutrients and don't need to carry out active metabolism, and so they are much bigger.
I took some of the examples from here, and for more technical information about the upper limits of cell size and plant cells click here.

All cells take nutrients in from their environment, including those of multicellular organisms, even mammals, so your second paragraph is irrelevant. Viruses can be packages with enzymes such as reverse transcriptase and integrase, etc. so your third paragraph is incomplete. Your fourth paragraph is somewhat true, but neurons would be a better example. Also you make no mention of the hypothetical size limit of all cells due to surface area to volume to diffusion rate limits. And your answer lacks references. I know the OP accepted the answer, but it lacks quality and should consider removing,

I agree with you @AMR that this topic is broad. I added reference to some more detailed article for the specifics. I think the answer fits the question. A more specific answer will meet a more specific question.

@AMR 's arguments are valid but you can answer them if you explain a parameter regarding the shape: surface area/volume ratio. While increasing surface area will allow a greater chance of nutrient uptake and synthesis, increase of volume will result in higher energy consuption. The cell has to strike an optimum. Therefore bigger eukaryotic cells are dependent on organelles for energy.


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DNA Topology. Question on twists and writhes
Hi guys there is a question which has been driving me crazy ever since I saw this video(https://youtu.be/az2c6UbEdug). At 4:50 the guy says that when a right-handed circular DNA starts forming a right handed interwounding writhe the DNA must adjust by twisting more(You can see the number goes up to 8 from 5 in the equation) and that when an interwounding writhe is done in the opposite direction it must twist less. To me this doesn't make sense at all. I thought that as you interwound to the right the twisting should lessen and when you interwound to the left the twisting should increase. Can someone explain(or show a very clear diagram/illustration which explains this) please??

It is all explained here in Wikipedia. If you want to make a 3D model of your own, you can use two pieces of tygon tubing (like the rubber hose for a Bunsen burner), that are both circularized and attached with connectors that can be opened and closed--that lets you simulate nicking and re-sealing the strands.

source: Stack Exchange

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

sort: votes


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Why does heating kidney beans at a low temperature potentiate the toxicity of phytohaemagglutinin?
I recently found out that red kidney beans contain a relatively high amount of the toxic lectin, phytohaemagglutinin.
An article on phytohaemagglutinin on the FDA website states:

Several outbreaks have been associated with "slow cookers" or crock pots, or in casseroles which had not reached a high enough internal temperature to destroy the glycoprotein lectin.
It has been shown that heating to 80°C may potentiate the toxicity five-fold, so that these beans are more toxic than if eaten raw.

What I do not understand is how the toxicity could increase if the beans are cooked at lower temperatures in a crock pot. I would understand if the toxicity remained the same (that is, not be deactivated), but I thought a toxin is nonliving (i.e., unable to grow and reproduce) since it is not a bacteria?
I know nothing about biology, so I am utterly confused.

The source quoted is the first edition (2009) of the FDA's Bad Bug Book.  The second edition (2012), no longer asserts that the toxicity increases over the raw state when heating to 80°C, nor does it contain the assertion that "Undercooked beans may be more toxic than raw beans."

@mgkrebbs Nice find. I am still curious about how this would be possible.

I am a Snr lecturer and a PhD candidate. Currently, I am putting my theses together. My research area involve in part the kinetic degradation of lectins in neglected and underutilized legumes. I  also looked at the possibility of using irradiation to produce complexed degraded starches  to inactivate lectins during low temperature extruder cooking.I observed in some of the extruded samples that lectins have actually potentiated up to about 50%. I was confused. I know lectins are proteins so they are supposed to denature when heated. I was looking around to see whether someone has made similar observation and I saw that indeed somebody has reported similar observation. I was so over joyed but it was short lived-no explanations were offered.  I now offer a possible explanation. Yes, lectins are proteins(or glycoproteins) and like most proteins their tertiary and quaternary structures are 3D. So the 3D forms have a couple of smaller subunits, woven together into the giant super structure(lectin). In the 3D form, most of the binding sites are "buried" or not fully exposed. It is possible that these smaller units have binding sites for carbs and are best positioned to present their ligands for  exposure and maximal binding when the 3D structure begins to "melt down". This melt down occurs at low temperature when denaturation has actually started.  Thus, the greater the exposure  number of subunits bearing the binding sites, the greater the potentiation. My work used low temperature extrusion cooking and the observation occurred in the extrusion cooking.
I just hope this suggestion is adequate. That is indeed the explanation I am going to offer for my observation anyway. Wish me best of luck!
Bye!

Welcome to Bio. On this site we encourage the use of references,  links to websites etc. to back our answers up and to allow other users to do background reading on your answer.

Additionally: Can you please remove all content about your PhD and so on which is not important to answer the question?

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Do animals demonstrate target practice (i.e., playful accuracy behavior)?
Do animals demonstrate any sort of accuracy-motivated play? (please provide examples!)
Consider most human sports and related hobbies. Most share the common goal of hitting a target or being accurate, and in the case of organized sports, points are typically awarded for being accurate. Archery, firearm past times, football, soccer, basketball, hockey, baseball, tennis, billiards, bowling, darts, beer pong, horseshoes, and countless other examples all are based on competitive accuracy.
Humans seem to be obsessed with accuracy in our competitive past-times. Examination of more ancient sport interests demonstrate less preoccupation with accuracy (though of course there is variation between cultures -- see here or here, ), and perhaps just more with demonstrations of strength and dominance. However, competitive accuracy was alive and well in ancient times: boxing, sword fighting, lacrosse, hoop rolling, golf (and Chinese equivalent Chuiwan), and others already listed are just a few examples of accuracy games with more ancient origins. It seems, then, that the human species has  had a fascination with accuracy for a long time.
However, do animals have the same (or really any) preoccupation with accuracy? I've seen countless examples of animals 'playing' or competing (e.g., pets & captive animals playing with toys & enrichment objects,  young males of various taxa sparring or wrestling, whales playing with their food, monkeys sheep herding on dogs, etc.), but is there any evidence or example of wild animals playing 'games' based on accuracy?

No need to comment on reasons why animals play. I understand that the bulk of animal 'play' is preparing them to be successful adults & that accuracy would typically not be immediately relevant for most animals. (Though bears trying to catch salmon, chameleons trying to catch insects, & osprey diving for fish are just a few examples where accuracy is necessary). In these cases, 'practice'  would not really be competitive or playful tests of accuracy, but rather just failed attempts to gather food. I'm curious if more playful examples of tests-of-accuracy exist in the animal kingdom?

I guess it is unlikely that playful tests of accuracy really developed before the evolution of hands and feet that are more amenable to throwing objects. Still, I could imagine instances where accuracy games involving spitting, rolling, fishing, insect-catching, etc.  could exist

Nice questions, but I voted to close. The questions are each quite broad individually, and you stack three distantly related queations on top of each other.  Please ask specific questions, one at a time. In its current form it's too broad to even start a partial answer attempt. Also, consider other SE sites. E.g., the history of human play is not on topic here.

I guess so yes, just develop them in independent questions with the appropriate background info targeted to each question. Simply copy-pasting the same text twice wouldn't be too constructive.

Voted.  Good luck!

Voted to reopen - though I'd suggest the question would benefit from reducing the amount of text... right now it's fairly substantial reading, that can put people off reading it properly...

One example that comes to mind is archer fish. There is evidence that they improve with practice, but they practice on targets that are food items, so I'm not sure whether that counts as practice with respect to your question. Interestingly, there's also some evidence that they can improve their accuracy simply by watching other archer fish succeed.

Does this count?
https://www.telegraph.co.uk/news/worldnews/northamerica/usa/2508756/Dolphins-play-with-bubbles-in-Florida.html

The playful creatures create the bubbles with their blowholes, then
  chase and swim through them.

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Are there fundamental differences between the adaptive immune systems of higher primates and other mammals?
I recently attended a Leukemia and Lymphoma Society lecture in which one of the lecturers indicated that there are fundamental differences between the adaptive immune systems of higher primates and other animals.
The Wikipedia article on adaptive immune system seems to indicate that mammals share very similar adaptive immune systems.
I understand that there are (minor) differences between the B cells and T cells (and other cells) of different species, and that two species can differ in their susceptibility to a particular kind of pathogen (virus, bacteria, whatever), depending on small differences in cell surface proteins, etc.  I am not interested in these kinds of small differences.
Rather, I would like to know if there are any fundamental differences between the adaptive immune systems of humans (and other higher primates) as compared to other mammals.  For instance, are there particular kinds of adaptive immune cells in primates that don't appear in other mammals.  Or are there fundamentally different mechanisms (e.g. the mechanism of T-cells activating B-cells) or lymphatic system organs that are markedly different in higher primates as compared to other mammals.
In short, are there big differences in the immune system of higher primates that make them stand apart from the other mammals in the same dramatic way that thumbs and intelligence seem to separate them from other species?

When the lecturer said other animals, were they specifically referring to other mammals or did they just say other animals? If other animals that can mean everything from fish, jelly fish, sponges, corals, reptiles, birds, insects, worms, etc., so then yes there are differences. If they specifically said other mammals, then there may be subtle differences, but in research animals such as mice, it is very similar. They may have meant the constant regions of antibodies, as these are unique to the species and can actually be exploited in immune assays.

In fact, it is often referred to as the vertebrate immune system. This might help: http://www.ncbi.nlm.nih.gov/books/NBK2388/

I am not aware of a discriminatory feature between primates and all other mammals. However, there are significant differences for some animals. For example, the anti bodies of camelids and sharks consist of the heavy chain only, or the antibodies of sea lampreys are not of the immunoglobulin protein family.
Those differences have been exploited for biotechnology.
consider this review: http://www.nature.com/nbt/journal/v23/n10/full/nbt1127.html


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Do ants use something similar to the honey bee "waggle dance" to instruct the rest of the colony where to find a food source?
In the 20 years since we built our home, we've just recently had our first ant infestation.
I'm familiar with the fact that ants leave scent trails to find their way back and forth between the colony and a food source.  So in my limited experience with ant eradication, I assumed that by taking away the empty ice cream bowl and scrubbing the scent trail which lead to it off the kitchen counter (multiple times with different household cleaning products) the ants would quickly give up their search.
My assumption was that the oncoming foragers would be confused by the abrupt end of the scent trail and wander aimlessly in the gap between where the trail had been scrubbed away and the former location of food.
However, what I’ve observed again and again is ants continuing to move across the scrubbed counter to the exact location of where the food used to be -- as if they didn't need the scent trail.  Their only confusion seems to be the lack of food at that spot.  This behavior will continue for several hours after the removal of whatever food had been there, despite multiple eradications and vigorous scrubbings of where the original trail had been.
Ants follow odor plumes to food sources according an answer in another Biology Stack Exchange post.
(Can ants sense food from a long distance?)
And from a link in the same Biology Stack Exchange post “If they [patroller ants] didn’t return to the nest, departing foragers would know it wasn’t safe to go search for food.” and “The ants can take advantage of sudden windfalls of food, but they don’t waste energy and resources if there’s nothing there.”
(https://wikkorg.wordpress.com/2015/04/23/ants-swarm-like-brains-think/)
Here are my questions:
Are ant scent trails strong enough to withstand multiple washings with soaps, detergents and disinfectants?
Can ants detect airborne food molecules in very small parts per million, even after the food and its odor plume have been removed?  If not, do ants use something similar to the honey bee "waggle dance" to instruct the rest of the colony where to find a food source?  Or both?
Why and how do they keep coming back to a place where there is no food, especially if (eradicated) members of the colony are not returning?

I know that some other Hymenoptera, including ants, have primitive waggle dance-like behaviours that are used for recruitment of workers to food sources. I don't know if they can convey spatial information though, but will try to find out more. The book The Ants by Hölldobler and Wilson is probably a good bet for more information.

I can only help you on one question about if ants perform a similar communication such as the "waggle-dance" to tell other ants if there is food elsewhere?
Ants will send out scout ants or forages, which will go out in search for food. The ants will lay a pheromone trail, by tapping their abdomen on the ground, like breadcrumbs. If the ant has found a food source, they will taste the food and take part of the food and store it in their crop. The ant will take the food sample and re-trace her trail, making it more detectable when returning to the food source. Once the ant reached the nest and finds another ant, she will regurgitate the food from her crop and position it between her mandibles. She will go towards another ant and exchange the food and pass it on to the ant in a "kissing" motion. This is called trophallaxis, where there is a donor, the scout or forager ant, and a recipient, the ant back at the nest. The ants will then follow the trail the scout first put down and will eventually create a motoway of food going to the nest.
Look up people like Nigel Franks and John Sudd - The behavioural ecology of ants.
The lives of ants - Laurent Keller and Elisabeth Gordon
The Earth dwellers - Erich Hoyt
sciencedirect.com/science/article/pii/0003347295801405 about trophallaxis in solenopsis ants sciencedirect.com/science/article/pii/037663578290050X about trophallaxis in Myrmica ruba
Hope that helps.

can you add some links to references or the sources that you indicate? interesting answer...


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Why are sequencing reads shorter than PCR products?
I have desinged and tested primers for RT-PCR, then purified the PCR products from the gels and send them to sequence at GATC (SUPREMERUN) using the forward primers.
After blasting the reads to refseq, I see that they are ~30% shorter than the PCR product. Example:
PCR expected length = 182 bp
Read length = 133 bp
I must mention that in the gels the expected PCR sizes were ok.
Does anyone have an idea what is the reason for this decrease in length?
Thanks

https://www.researchgate.net/post/My_PCR_product_is_163_bp_but_when_it_was_sequenced_multiple_samples_used_it_appeared_like_it_is_133_bp_what_could_be_the_problem

Reliable sequencing reads start usually 50bp downstream from start of primers. Which means that 180bp-band (on the gel) sequenced with one primer will yield readable sequence in region 50-180bp (130bp length). Also I notice that sequences usually reported somewhat before reliable data, i.e. clean data starts after 52-55bp, but sequencing reports basepairs downstream from 48bp after primer start.
If you need whole-band sequence, you will have to sequence with set of two primers, each in different direction. Since you PCR this band, you already have your sequencing primers.


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Does medication make the body dependent?
First of, I know of course that certain medication can cause an addiction if incorrectly used. But as far as I understand it, drugs prone to cause addiction have some agent in it, that makes them addictive.
What I am interested in is a bit different though: If a drug "helps your body" do something your body can not or only insufficiently do alone, does it get dependent on this drug, even if the drug does not have addictive substances in it?
Or in other words: Can the human body unlearn something because of the fact that medication helped it do it for some time?
Edit: To make the question a little more clear, I can give the following example: I recently received medication containing Etilefrine, which contracts my blood vessels and thus prevents me from fainting in certain situations. If I take this medication regularly for a year and the suddenly stop it, could it be possible, that my blood vessels "forgot" how to contract on their own?

Stopping drugs/alcohol "cold turkey" can be fatal - drug dependency is a common problem

@rg255 I checked the Wikipedia article on it, along with the one on Drug withdrawal and it had some useful information in it. However, the articles tend to discuss drugs containing addictive substances. I would also be interested in drugs without those substances.

You have now specified your question, but a different thing you might be interested in is steroid withdrawal and what can happen if corticosteroids are stopped abruptly.

@YviDe I gave steroid withdrawal a look, it is a very interesting subject and roughly the thing I asked about. Thank you!


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How much do crocodiles eat?
How much do crocodiles eat? The closest I found to an answer was on German wikipedia, where it says that adult nile crocodiles eat "only about 50 full meals a year." While interesting, without knowing what a full meal is this is meaningless. So how much does an adult crocodile actually eat?
I think relevant other questions in this context are:

Do all adult crocodiles (or even all crocodilia) eat roughly the same (corrected for body mass)?
Some crocodiles apparantly eat fruit and seeds on a regular basis*, is this is a relevant part of their caloric intake or just a "vitamin supplement"?

*paywalled article, I only read the abstract

re the close vote: a) I've added the additional questions because I don't think one can answer the question meaningful without at least adressing them (but could be wrong) b) a comment why exactly the vote to close would be appreciated.

fwiw, english wikipedia on crocodilia states "10-20% of what a lion needs" witht this paywalled source: http://onlinelibrary.wiley.com/doi/10.1111/j.1469-7998.1986.tb01518.x/abstract someone with access could use this maybe?

full meal= bloating with days of digestion


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Examples of seeking behavior by brainless animals
Are there any examples of brainless animals (e.g. jellyfish) exhibiting seeking behavior, such as following smell or light gradients towards food, or following hormones towards mates?

Yes, there are plenty of examples! We refer to this seeking behaviour as taxis.
Taxis
There are many types of taxis such as chemotaxis (attracted to chemical stimulus) or phototaxis (attracted to light). A complete list of taxis can be found on wikipedia > taxis.
For the purpose of this answer I will restrict to chemotaxis only

Chemotaxis (from chemo- + taxis) is the movement of an organism in response to a chemical stimulus.

Chemotaxis in Bacteria
Chemotaxis is very common in bacteria such as E. coli for example (Macnab and Koshland 1972, Wadhams and Armitag 2004).
Chemotaxis in Plants
Chemotaxis is also observed in plants such as rhibozium spp (Currier and Strobel 1976) for example
Chemotaxis in eukaryotes
Chemotaxis is also found in eukaryotes such as in Amoeba or Tetrahymena (Köhidai 1999,Bagorda and Parent 2008) for examples.
Chemotaxis in animals that have "primitive" brains
Nematodes (Ward 1973) and plathelminthes (Bone 2012) for example show chemotaxis.
Chemotaxis in "brainless" animals
Evidence of chemotaxis also come from Echinodermata (sea stars, sea urchins and others) (Miller 1985).
Echinodermata have quite definitely no brain!


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Determination of Ageing by ECG inclusions/exclusions?
I am studying ageing and considering ECG signal because of its high sensitivity in theory (escardio). Some factors

Sensitivity
Gender
Medical treatment
...

Benchmark:
RTG dental + wrist uncertainty $\pm$2 years. Etc tooth washing, and hardness of drinking water affect much the dental health. Exposure to the ionisative radiation is problematic so less radiative approach would be nice.
ECG
Cardiac characteristics by ECG signal in power spectrum, having greater uncertainty than RTG dental 2016 because no sufficient exclusions/inclusions and too much exclusions covering data segments of autonomic nervous systems.
Processes to be excluded from the ECG signal

respiratory process
heart beat itself
some cellular-tissue processes

Some cellular-tissue processes

ROS determination ...
some genes about lipids and their characteristics with ageing in metabolic syndrome
decreased replication of cellular ageing
DNA replication stress, genome instability and aging
MICCAI 2012 Workshop on Novel Imaging Biomarkers for Alzheimer's Disease and Related Disorders

Low-Cost Targets

internal physiology of cardiac events in association with ...
cardiac and brain imaging makers related to substance use disorder, HIV, and aging (Stanford)

How can you determine aging by biochemical test and imaging?

I think you need to focus the question a little more. As it stands you list methods to study aging and then summarily ask how to study aging. Perhaps pick a specific technique and ask a specific question about your problems with that specific technique for better reception. I think going down a list of techniques and giving them each a thorough exposition warrants an answer that is too broad.

@Kendall Yes, you are right. I put the focus on Cardiology but including inclusions and exclusions. ECG signal has the great potential in high sensitivity. (escardio)


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Examples of animals with 12-28 legs?
Many commonly known animals' limbs usually number between 0 and 10. For example, a non-exhaustive list:

snakes have 0
Members of Bipedidae have 2 legs. Birds and humans have 2 legs (but 4 limbs)
Most mammals, reptiles, amphibians have 4 legs
Echinoderms (e.g., sea stars) typically have 5 legs.
Insects typically have 6 legs
Octopi and arachnids have 8 legs
decapods (e.g., crabs) have 10 legs

....But I can't really think of many examples of animals containing more legs until you reach 30+ legs in centipedes and millipedes. Some millipedes even have as many as 750 legs! The lone example I am aware of, the sunflower sea star, typically has 16-24 (though up to 40) limbs.
So my question is: what are some examples of animals with 12-28 legs?

One will need a good study of the distribution of number of legs (and the sample size used to build this distribution) before saying anything. For the moment the presence of a "distributional gap" is an opinion and is not evidence-based. I am voting to close as such. The question is interesting though!

@Remi.b: you're right about your points concerning distribution. So instead, I've modified the question to focus on simply: why are there not examples (or more examples) of animals with between 12-28 legs. ...Visualizing the distribution of species and their leg numbers would be very fascinating, though wayyy too much work to do accurately).

Yes, I realize how much work it would be but without that it makes little sense to speculate on why are there not examples (or more examples) of animals with between 12-28 legs unless we know whether or not this is to be expected from the little sample size (taken pseudoreplicaiton into account) that is available.

@theforestecologist Birds and humans, like all Tetrapoda, have 4 legs. This distinction you made from legs and limbs makes no biological/zoological sense.

As a couple of counterexamples, species in the classes Symphyla (Pseudocentipedes) and Pauropoda within Myriapoda have 8-11 and 12 leg pairs respectively, so between 16 to 24 legs (sometimes with one or two leg pair stronlgy reduced in size).

(species in Symphyla, from wikipedia)
Another common and species-rich group with 14 walking legs (7 leg pairs) is Isopoda.

(Isopod, picture from wikipedia)
You also need to define 'legs' for the discussion to be meaningful. As you say, decapods have 10 legs on their thoracic segments (thoracic appendages), but they can also have appendages on their abdomens (Pleopods/swimming legs), which will place many decapods in the 10-20 leg range.

(Decapod abdominal appendages/legs in yellow, from wikipedia)
So overall, in Arthropoda, having 12-28 legs doesn't seem all that uncommon. There are probably other Arthropod groups besides those mentioned here that also have leg counts in this range.
However, for a general account, the most likely answer (if there is indeed a relative lack of 12-28 legged animals) is probably evolutionary contingencies and strongly conservative body plans within organism groups.

Also velvet worms.

The now-extinct, Hallucigenia had 7-pairs (or 14) legs.


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What causes the opaque green colour in Lepidoptera?
Link here to what I mean by 'opaque' colouration on the insect, the colour intensity remains constant despite changes in light intensity and angle (not shown by the picture but the moth exhibits this in the field). This is different to 'metallic' colouration on other moths like the Forester moth (image here), where the colour intensity changes with light angle and intensity.
Through reading R.F. Chapman's book ('The Insects:
Structure and Function'), I know that metallic colours are caused by interference patterns produced by the micro structure of the scales, the book says this is how most higher frequency colours are produced, including green in this category. Obviously I've looked for pigments that could give this colour but I haven't found anything that is produced in insects.
So my question is: Is there a pigment that gives this colour in the insect and if so, what is it?

According to this paper, green pigments are found in lepidoptera. The study focused on Geometridae, and found that the primary pigment in emerald moths, such as Hemistola chrysoprasaria is also found as secondary pigment in Pseudoips prasinana. The authors dubbed the substance 'Geoverdin' and suggest it may be a derivative of chlorophyll consumed during the larval stage. I cannot find any further studies mentioning 'geoverdin' or its chemical identity.


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Will dissolved proteins pass through a 0.2 micron filter?
Given that there may be exceptions, can you usually expect protein to pass through?

Many proteins will pass through a 0.2 micron filter. If the proteins aggregate or if they stick to the filter material because it is charged, they may not.
Barring the above, a 0.2 micron filter will allow proteins up to 200kd to pass through.  There are some proteins that are larger.
Editing with some source material.
Nice Presentation on Pore Sizes and Membranes Here
Graphic from that presentation:

Stanford ppt link is broken :(


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How is AMP "recharged" to become ATP in a cell?
I understand that after the translation stage of ribosomal protein synthesis, tRNA molecules are floating in the cytoplasm without attached amino acids until they find the correct aminoacyl tRNA synthetase enzyme which revitalizes them.
However, in this process the enzyme takes an ATP molecule and returns an AMP (not ADP) molecule. It's been my understanding that an ATP's energy is normally harnessed via removing a single phosphate group and leaving an ADP molecule. Processes like respiration and photosynthesis deal with the conversion of ATP to ADP and vice versa. I understand that in removing the extra phosphate group to get an AMP more energy is released, but that also means that more energy has to be used to convert the AMP to ATP.
Does the cell convert the AMP to ADP, which will ultimately become ATP in respiration, or does the cell use some retrofitted respiration/metabolism to revitalize the AMP?
I would expect the first option but it would take energy (most likely from an ATP) and I would expect the amount of energy released from an ATP becoming an ADP to be different from the amount of energy released from an ADP becoming an AMP (so an ATP becoming an ADP would take more or less energy than would be required to make an AMP become an ADP, leading to inefficiencies). The other possibility (that I can see) is that the AMP is just used as a nucleotide in DNA and RNA, but I don't think that the numbers add up there. I've looked around but I can't find an answer.
So how do cells convert AMP to ATP? Also I was told that the ATP to ADP conversion is the general power-conversion. Is that not the case, or is this just some rare occurrence when AMPs are involved in power conversions?

Are you interested here in plant cells, animal cells, etc? Bare in mind for many cell types, ADP are largely converted to ATP by ATP-synthase, but AMP plays a crucial homeostatic roll, and coupled to adenylate kinase, helps to, accoring to this article, optimize the ATP-synthase process (I believe they're studying plant cells there).

I'd be interested to learn about AMP conversions in both plant AND animal cells, but I'll settle for whichever is more common (as in whichever one that uses AMP molecules more frequently).

Your statement about AMPs possibly being used in DNA/RNA synthesis is wrong, those are built with nucleotide triphosphates, including ATP, TTP, UTP, CTP, and GTP. Nucleic acid synthesis is similarish to your tRNA question because each triphosphate loses 2 phosphates when added to the growing DNA/RNA chain. If the chain is ever broken up, the nucleotides are released as monophosphates.

@user137 Nucleotides do, in fact, have only one phosphate group. Molecules like ATP and GTP have three. Nucleotides have ONE phosphate group, a ribose sugar, and a nitrogenous base

@jacob Nucleotide vs Nucleoside is just being pedantic. The point is that three phosphates go in, 2 get thrown out. See this image

@jacob It was an obvious typo, since "nucleotide triphosphates" would contain four phosphate groups.

AMP is first converted to ADP in the reaction
AMP + ATP $\leftrightarrow$ 2 ADP
catalyzed by adenylate kinase. So one phophate group is transfered from ATP to AMP, resulting in two ADP molecules. The ADP formed is then used to synthesize ATP as usual, by the mitochondrial ATP synthase or by the glycolysis enzymes.
For other nucleotides and deoxynucleotides, the monophosphate form NMP are usually phosphorylated to NDP using ATP, catalyzed by various kinases. For example, UMP and CMP is handled by the enzyme CMPK. Note that this is essentially the same type of reaction as adenylate kinase.
Regarding the energetics, the above reaction is only slightly favorable (at equal reactant concentrations) with $\Delta G=-2.6$ kJ/mol. In most cells, ATP concentration is much higher than ADP though, which helps drive the adenylate kinase reaction forward. See this site where you can investigate the energetics more closely.

Roland, where the ATP is found if it is not synthesized (оxidative phosphorylation needs ADP for synthesis of ATP)?

@AlexanderBestavashvili, I'm not sure I understand you question, but there is plenty of ADP, since most reactions that hydrolyze ATP produce ADP. The adenylate kinase reaction just takes care of the more rare case where AMP is produced instead of ADP.

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


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Reason for aquatic plant roots
My question is about why aquatic plants have roots. At first they seem a bit superfluous to me because leaves of the plants could just absorb nutrients directly from the water thereby skipping a need for root function that land plants have to pull nutrients from the soil. I then wonder if nutrient trafficking is the reason for the root system as diffusion may not occur efficiently through thick leaves.

Also consider alternative uses, such as anchoring/staying in one place.

I did consider that and that makes sense but doesn't solve why roots still are the nutrient absorbing part of the plants rather than the entire plant.

According to this article, Bladderworts have evolved this ability.


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"Heterozygotic expection" - when heterozygote differs from both homozygotes, but homozygotes are similar
For simple 2-alleles genetic model {a,A} and corresponding quantitative trait Q is typically true that
Q(aa)>=Q(aA)>=Q(AA)
or conversely
Q(AA)>=Q(aA)>=Q(aA).
For example, dominance means that Q(aa) < Q(aA)=Q(AA) , recesivity Q(aa)=Q(aA) < Q(AA) ; in additive models Q(aa) < Q(aA) < Q(AA) etc.
The situation when Q(aA)>Q(aa)~Q(AA) is atypical in biology ("heterozygotic expection ?", "uncooperative alleles ?"). Known example is HBB gene (heterozygotic form gives resistence to malaria but homozygotic mutation form is sickle-cell anaemia). But this is weak example only, because f is evolutionary advantage, not a measurable  phenotypical or biochemical trait.
QUESTION 1: Are there any systematic reviews about this atypical phenomena? (about "heterozygotic expection")
QUESTION 2: Is there a standard scientific term for this phenomena?

You question is a bit unclear, and I think there might be a couple of mistakes in your inequalities. However, I think you are looking for the terms Overdominance (also called Heterozygote advantage) and Heterosis (also Hybrid vigor). Both of these concepts imply that heterozygotes and/or hybrids have a phenotype that lies outside of the range described by the homozygotes (or, for heterosis, either parent or parent population).
Here is a section from "Genetic Dominance: Genotype-Phenotype Relationships" from Nature education - Scitable, which has a bit more information and a couple of references:

In particular, the phenomenon known as overdominance occurs when a heterozygote has a more extreme phenotype than that of either of its parents. Indeed, in a few examples, a trait that shows overdominance sometimes confers a survival advantage in the heterozygote (Parsons & Bodmer, 1961).

You will find more information about overdominance and heterosis in any textbook on evolutionary biology, e.g. Futuyma's Evolution. There are also lots of relevant papers on the subject, and this one might be a nice example and starting point:
Frascaroli et al. 2007. Classical Genetic and Quantitative Trait Loci Analyses of Heterosis in a Maize Hybrid Between Two Elite Inbred Lines. Genetics 176(1): 625-644.


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Why does Citric Acid occur in Citrus fruits?
Why is there so much citric acid in citrus fruits? And how did it evolve i.e. what did it come from? Is it a by-product of the ripening process?  Why have citrus fruit evolved a particularly high amount of citric acid compared to other fruits? Was it due to particular selection pressure for acidic fruits or was there a genetic bottle neck that caused this such as human cultivation?
I've been trying to search for this but google scholar isn't throwing up anything so I'd really appreciate some help.

This is a related question but I don't think the answer there has addressed the evolutionary aspect of acid accumulation.

Thank you for the link anyway, the answer may give me some useful information.

It's been a difficult search, honestly. I'd like to think the citric acid preserves the fruit in it's native growing condition; lemon trees originate in Asia, for example (high humidity, lots of bugs, etc.). I've come up largely empty-handed!

Actually citric acid is not only available in citrus fruit but also in pretty much any living thing. it is an important intermediate in Krebs cycle, but I guess the main reason that it is available in high concentrations in citrus fruits is because citrate is an inhibitory compound for phosphofructokinase, that means it stops the glycolysis and hence it makes it hard for bacteria to use the fructose available in the fruit body.
Source:
 Stryer, Lubert; Berg, Jeremy; Tymoczko, John (2003). "Section 16.2: The Glycolytic Pathway Is Tightly Controlled". Biochemistry (5. ed., international ed., 3. printing ed.). New York: Freeman. ISBN 978-0716746843.

Then why haven't more fruits evolved this? I'm aware that citric acid is found in all living things, I apologise if the wording is misleading. My question more why does citric acid occur in such high concentrations in citrus fruits compared to other fruits.

Actually, I think  it is more a question of diversity. most of the fruits have their own preservatives, in citrus fruits case it's citric acid.in some fruits it's high sugar concentration.in some other it's vitamin C. it's a matter of diversity and the reason that other fruits went down another path is probably a matter of chance and environment and previous terms.
I hope I had answered conveniently.

@Phototroph I think by asking "Then why haven't more fruits evolved this?" you are making your question opinion-based. You might want to read http://biology.stackexchange.com/questions/35532/why-do-some-bad-traits-evolve-and-good-ones-dont for help. In short, evolution is not meant to make organisms better, but just to become different from others. Its natural selection by which better ones survive while worse ones can't.

I realise how evolution works, apologies if my wording doesn't make it clear. Haven't contributed further to this because Shayan's comment more or less answers my question (it's a question of diversity), but have left this open to see if anyone else has anything further to contribute


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What fills the spaces between non-fused sacral vertebrae?
What is in between the sacral vertebrae before they are fused?
I have looked and found no specific descriptions. If it is simply cartilage, what type of cartilage?


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BWA-MEM single strand or doublestrand alignment
In whole genome secondary analysis does BWA-MEM use a double stranded fasta reference or are reads aligned to only one, single stranded fasta reference?

BWA-mem (like most aligners), takes a normal single-stranded fasta file (I've never seen one with both strands listed) and aligns to both strand.

This means that BWA-MEM takes into consideration the complementary strand of each single stranded read prior to alignment?

Yes, all normal aligners do this.


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What is a tardigrade "in tun form"?
While reading this article about tardigrades that had been previously frozen, I came across some verbiage I wasn't sure of and couldn't find any real explanation given the context. The article kept making mention of the tardigrades "in tun form", yet the only references I could find to the meaning of tun dealt with weight or casks (like for holding liquid).
So does tun mean cask (like a casing) in this context?

I was wondering the same thing for a good long while, but I have come to the same conclusion that tuns are a folded-up version of the tardigrade that slows down the metabolism of the creature. >>>Tardigrades are microscopic, yet almost invincible one-celled organisms.-Anonymous

From Illinois Wesleyan University:

One way in which tardigrades have adapted to various types of
  environments, has been to reversibly suspend their metabolism. This
  state is known as cryptobiosis [ 'hidden life' (Clegg, 2001) ] and is a truly deathlike state.
  Metabolism lowers to 0.01% of normal or is entirely undetectable and
  the water content of the body decreases to less than 1%. [...]
The most intensely studied type of cryptobiosis is anhydrobiosis, a
  form of cryptobiosis initiated by desiccation. [...] Anhydrobiosis is an almost complete
  loss of body water and the animal can stay in this state for an
  extended period of time. Tun formation, a vital part of the process [Fig. 1.],
  results in a body that is constricted and folded. The first step is
  invagination of the limbs, longitudinal contraction of the body, and
  infolding of the intersegmental cuticle. Wax extrusion covers the
  surface and may help to reduce transpiration (water loss by
  evaporation). The tun formation process requires active metabolism. [...]

Fig. 1. Tardigrade before and after entering the tun state. Note the decreased body length and infoldings. Source: Media & Society Journal.
Reference
- Clegg, Comp Biochem Physiol B Biochem Mol Biol (2001); 128(4): 613-24


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Can an enzyme be activated without allosteric inhibition or activation?
Are there ways by which an enzyme may be activated or inhibited by non substrate molecules other than allosteric activation or inhibition?

Apart from what Phototroph mentioned in their answer (competitive and non-competitive inhibition), an enzyme can be activated/inhibited via covalent modification of the protein (post-translational modification) such as phosphorylation by protein kinases (phosphorylation is the most common modification).

Yes, competitive inhibition is another form of enzyme inhibition. The inhibitor binds to the active site here, as opposed to allosteric inhibition, where it binds to a secondary site. An example of an inhibitor would be the cyanide ion (CN-), which inhibits Cytochrome C oxidase, preventing electron chain transport and thus ATP production. Note this ion is different from the substrate, oxygen.


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How does cytochrome c oxidase inhibition cause cell death?
I realise the inhibition of cytochrome c oxidase prevents the release of H+ ions into the intermembrane space, and that the ion gradient is required for ATP synthase action. However, I'm not sure how this causes cell death.
Does this:
a) Prevent oxidation of Cytochrome C, preventing electron movement the cytochrome bc1 complex, which in turn prevents electron movement from earlier parts in the chain, shutting down the electron transport chain altogether? Thus, no ATP is produced and the cell dies due to lack of ATP.
b) Prevent oxidation of Cytochrome C, but not preventing oxidation in the other protein complexes*, merely reduce the number of H+ ions available for ATP synthase action, lowering the amount of ATP produced, and the cell dies due to low ATP levels.
c) other.
I realise in either case, the ATP count is merely lowered, as ATP is produced by other methods, so my statement 'lack of ATP' is not totally explicit.
*This being the case, how are the released electrons dealt with by the cell? Are there electron acceptors to remove this?

The cell dies due to lack of ATP but the organismal death happens because the brain and the respiratory centre is affected. Neurons are quite sensitive to ATP loss.

Thank you. Do you know exactly how inhibition reduces the amount of ATP? Is it scenario a), b) or other?

Inhibition is rarely binary - it's almost always subjected to stoichiometric effects. So the answer could be either option, depending on the amount of the inhibitor present in the system. If there is a huge amount of the inhibitor in the cell, it may more or less completely ablate ATP production by the ETC.
On the other hand, if there isn't enough of the inhibitor to shut down all cytochrome C oxidase, you'd only see a reduction in the amount of ATP produced by the ETC (which could still be sufficient to kill the cell).
It also depends on the type of inhibition taking place. Is it reversible or does it bind permanently? Does it degrade quickly? These aspects are also important to consider.


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How do you know which organisms are keystone species?
I know that keystone species are those that play a crucial role in an ecosystem, but since all species are interdependent upon each other and each occupy their own niche, aren't they all important?
How do you know which organisms are keystone species?

According to the wikipedia page, a keystone species is:

A keystone species is a species that has a disproportionately large effect on its environment relative to its abundance.

Thus, you could work out the keystone species in an ecosystem by sampling population size and and what size 'effect' the removal of the species from the ecosystem would have. If you standardised the units of 'effect' for all species in the ecosytem, the keystone species would be those with the highest effect/population fraction. I don't know if there's a critical size of this fraction for a species to be determined 'keystone', but if there is it would allow you to explicitly define a keystone species. This would rule out the problem of interdependency as you mention.

(Posting different answer as it gives a different approach to the question)
Re-reading this I think you were asking about how we'd infer these keystone species experimentally.
As a starting point, one could apply network inference on species counts in the ecosystem (https://doi.org/10.1890/09-0731.1, https://doi.org/10.1038/s41598-017-07009-x, https://doi.org/10.1016/j.ecolind.2015.11.031, as examples). This kind of study returns networks which represent the interactions between species - you could then search through these networks for species with many connections in the network. Removal of a species with many interactions with many other species is likely to have a greater impact than removal of a species with fewer interactions, suggesting these are keystone species.
I realise in your question that you sort of imply each species has an interaction with every other species in the ecosystem, but studies like the ones above show that this might not be true. Or at least, many of these interactions may be indirect, via another species.
After such a study you could apply statistical methods like Pearson's Correlation to work out the 'strength' of the interactions in the network. From this could identify species with many high-strength interactions as keystones. Alternatively you could attempt a parameter fitting on the learned network structure (as you can in the case of Bayesian Networks above), to try and predict what happens to the abundances of other species if you remove one of your candidate 'keystones'.
Hope that gives a more experimental angle on how to solve this question!


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Why do children prefer sweeter foods?
As we get older, we tend to lose our sweet tooth and become more tolerant to bitter foods, like vegetables. However, I never understood how this works. Why is it that children prefer sweeter foods, even some that adults may consider "too sweet"? In fact, is there any reason they would also dislike bitter foods, even when they can be beneficial to their health?
This just seems bizarre to me that the body would start out craving sweets and lose this later on. Are only humans like this? Is there anything suggesting that younger animals prefer sweet foods too, but like them less as they get older? Does this have any biological advantage or is it just random?

Your body start out craving for milk and lose this later, it often lose ability to digest milk at all. Why this should be bizarre? Human body needs change in time. Young children require a lot of energy to grow and to learn.

@Colombo explains one reason that I think is obvious. However, there has been some research done on this.
One other reason is because it would provide an evolutionary advantage in environments where calories are scarce. Also, sugar actually acts like a pain reliever. Studies show that giving sugar to babies and children during surgery act like a pain reliever.
The sweet tooth could be controlled by hormones secreted from the growing bones. Some common hormones like insulin also affect sensory centers in the brain. This explains why the sweet tooth goes away as an adult.
Reference
NPR -http://www.npr.org/sections/thesalt/2011/09/26/140753048/kids-sugar-cravings-might-be-biological

other reason is because it would provide an evolutionary advantage in environments where calories are scarce. Should't then fat taste sweet? fat = 9 cal per gram, sugar = 4.


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Aspirin - does it inhibit enzyme of thromboxane?
This is a diagram a friend showed me about the drug aspirin, where we were arguing which enzyme it prevents.

Aspirin is known to inhibit the production of prostaglandins. However, it also serves fit as a purpose to inhibit production of thromboxane.
My question is, does the drug inhibit enzyme a to prevent the production of both thromboxane and prostaglandins, or only enzyme B?

Aspirin and some other NSAIDs inhibit cyclooxygenase which is the first enzyme in the prostaglandin/thromboxane biosynthesis pathway if you consider first substance is arachidonic acid (a fatty acid). Generally, arachidonic acid is present in the form of a phospholipid, and if you consider that in the pathway, substance-Y is arachidonic acid and enzyme-A is cyclooxygenase.

From: Heckmann, Lars-Henrik, et al. "Outlining eicosanoid biosynthesis in the crustacean Daphnia." Front. Zool 5.11 (2008).


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What is the purpose of THC for a Cannabis plant?
Why does a Cannabis plant produce THC? This question is brought up drawing an analogy to nicotine in tobacco, where nicotine is developed by tobacco plants as a pesticide. Is THC a pesticide as well? I'm imagining that marijuana plants don't have rheumatoid arthritis.

It may also act as an insulation barrier for the plant to protect it from the cold.

Phytocannabinoids are found in an exceedingly wide range of plants, if that matters.

Apparently it is used by Cannabis sativa as a type of sunscreen as it absorbs UV light
https://www.reddit.com/r/trees/comments/2v79dv/science_sunday_13_wait_why_does_cannabis_have_thc/
https://en.wikipedia.org/wiki/Tetrahydrocannabinol


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What kind of changes "stays" in the neuron after the nervous impulse happened?
I often see in neuroscience textbooks about how the brain controls everything in the body with different tracts and etc, and it seems that information is always being transmitted, like there's no fixed place in which they are stored. So after the depolarization and repolarization what happens to the neuron itself? Does it depend on which neurotransmitter stimulated it? And extending a bit the question, what is exactly the difference between being stimulated by two different neurotransmitters?(supposed that the neuron has receptors for both and the neurotransmitters are the excitatory type).

TL;DR: There are many ways a neuron can change after a neural impulse happens including calcium influx, long term potentiation and depression, and G-protein coupled receptors. While not an exhaustive list by any means I'll give a brief summary of some mechanisms I know best.
Calcium Entry
There exist calcium channels that open in response to a variety of signals be it voltage depolarization (voltage gated calcium channels), neurotransmitter acetylcholine (Nicotinic-Receptor) or Both depolarization and Neurotransmitter binding (NMDA receptor). There is much more calcium outside the cell than inside the cell. Once inside the cell calcium binds to EF-hands in various calcium-binding enzymes like calmodulin. When calcium binds to the EF-hands of the calmolulin protein it activates and from there can interact with the other enzymes responsible for cell signaling and the effects can be quite diverse depending on what the neuron is responsible for doing and the specific signaling cascade it sets off.
LTP/LTD
I'll focus on the NMDA receptor(excitatory Glutamate/Glycine receptor) in the CA1 region in hippocampus. LTP (or Long Term potentiation) occurs when a synapse (connection between neurons) becomes stronger, meaning the post-synaptic neurons response to the same stimulus from the pre-synaptic neuron is stronger after LTP has occurred. LTD (or long term depression) is the opposite effect where a neuron's response to the same stimulus is weaker after LTD.
The LTP whole process is dependent on calcium entering through the NMDA receptor channel. When both glutamate and glycine are released pre-synaptically they open the channel,  allowing calcium ions to flow into the cell. However, If the voltage in the post-synaptic membrane is too low, Magnesium will get stuck in the channel blocking calcium (and the other ions too!). If the neuron has previously been stimulated and depolarized, by another neurotransmitter/receptor system like AMPA the voltage will be positive enough to pop the magnesium out of place and allow calcium into the cell.
Once calcium is in the cell it is bound to calmodulin which then binds to CaMKII (an enzyme activated by the calcium/calmodulin complex). This will cause a long and complicated signaling cascade which results in AMPA (the other excitatory glutamate receptor in the post-synaptic region) to be phosphorylated causing it to be more active. Furthermore the signaling cascade can cause an increase in AMPA receptor creation and subsequent insertion into the post-synaptic membrane. This of course results in LTP.
Many rules in biology one quickly finds exceptions and caveats to nice rules of thumb (In fact I learned of a few just by preparing this answer!) LTD (long term depression) can occur in the hippocampus as well, and is dependent on the influx of calcium! As paradoxical as that seems, there is a negative feed back loop dependent on the levels of calcium ions inside the neuron, such that strong pre-synaptic stimuli create LTP (potentiation) and weaker (lower frequency) stimuli cause LTD (depression) and rare or intermittent stimuli cause no response. (see this and this for reference).
G-Protein coupled Receptors
G-Protein coupled Receptors are more of a general family of proteins than a specific example. They are metabotropic receptors (meaning they do not allow Ion's to flow through them). Rather when bound they release an G-Protein, which like calmodulin binds to other enzymes and activates them allowing them to do their job. They  can respond to many different neurotransmitters (or more generally ligands) and can do lots of different tasks depending on the  on what type of G-Protein it releases.
I'll give the muscarinic(M2) receptor for acetylcholine as an example. This receptor is found in the heart and responds to acetylcholine release from the Vagus nerve. When the GCPR binds to the acetylcholine it releases its G$\beta$ unit and it binds to potassium ion channels in the heart. This causes the outward flow of potassium ions thus lowering the voltage( hyper-polarizing the heart cell).
Furthermore G-coupled proteins can even induce changes in how many are present in the membrane (i.e. they are self regulating). These are produced by internal signaling cascades and are thought to be the reason for tolerance of drugs. Take for example the $\mu$-opioid receptor (activated by morphine, heroine and other similar compounds). These drugs will induce changes in how well the protein response to the morphine and if enough exposure then the cell will actually take the receptor back into the cell body and thus off the membrane in a process called endocytosis. (source here)
Literature reviews worth reading include (all open access):

Calcium signaling
NMDAR meditated LTP/LTD
GPCR's

Excellent!!! Really liked your approach and all the links provided! I'll look into all of this


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What determines the shape of the center-surround receptive fields of retinal ganglion cells?
The wikipedia article about receptive fields of visual system tells us the following:

The receptive field is often identified as the region of the retina where the action of light alters the firing of the neuron. In retinal ganglion cells (see below), this area of the retina would encompass all the photoreceptors, i.e., all the rods and cones in the retina.

Then it shows some pictures

I understand the part where it says that the neurons firing increases as we put light on the center of the receptive field (for ON center type) and etc.
What I'm not sure about is the location of this circle; where is this circle that we put light on?
What I think might be the answer is that, as the quote says, the circle is the area of retina where we have the rod/cone shaped photoreceptors.
So this means that, for every ganglion cell, the photoreceptors connected to it are always shaped like a circle?

The center-surround structure is created by the horizontal connectivity of the horizontal cells (Periman et al., 2012)  that receive input from multiple photoreceptors (Fig. 1).

Fig. 1. Retinal patch showing the connectivity between a horizontal cell and photoreceptors. Source: Harvey Mudd College
The horizontal cell passes on the congregate output to the bipolar cell, which in turn drives the retinal ganglion cells (RGCs) that send their axons to the optic nerve and send the signal on its way to the brain.
The photoreceptors are connected in two concentric circles to the horizontal cell. When light stimulation of the inner patch (center) evokes an excitatory response in the RGC, and the outer circle (surround) inhibits this response, the receptive field is said to have an ON-center configuration. In the reverse scenario, it is OFF-center (Fig. 1). This center-surround configuration is one of the first visual processing steps in the visual system and enhances contrast in the perceived image.

Fig. 2. ON and OFF center-surround receptive fields. Source: Brain Connection
Reference
- Periman et al., Webvision. The Organization of the Retina and Visual System. Utah


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Identifiying a conserved residue in multiple PDB structures
I have a few hundred PDB structures of the same protein, and I need to identify a specific conserved residue in all of them.
Originally I wanted to extract the sequences from the PDB files with BioPython, align them and then use that alignment to identify the residue number in each PDB for my conserved residue.
But it turns out that is a bit harder than I expected. Parts of the sequence are often missing in the PDB. I don't see an obvious way to get a proper sequence out of the PDB files. Then there is the issue of mapping the conserved residue number back into the PDB file.
Is there any easier way to do this? It doesn't have to be BioPython, though that would be nice.

There are a lot of potential issues here. 1. your biopython script is struggling to handle missing sequences (you need an error handler). 2. you're using an unusual set of PDB files that are poorly formatted. I've tried to answer assuming that your PDB codes map well to uniprot. Let me know how it goes!

My approach to this problem would be to use VMD (Visual Molecular Dynamics), where you can load multiple PDBs, perform structural and/or sequence alignment and analyse residue conservation within one program.
VMD is a powerful molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. It is probably an overkill for what you want to do, but I find it rather intuitive to use and powerfull. I also has an amazing documentation and many step-by-step tutorials, starting from this basic introduction.
What you will specifically need for your problem is a MultiSeq 2.0 plugin that you can find under Extensions->Analysis->MultiSeq in new versions of VMD. It is a bioinformatics environment that allows you to load, display, and analyze both sequence and structure data for your proteins within a few mouse clicks. It also has a great set of tutorials to help you start! What you might find interesting for comparing many similar protein structures is an option to create, view and manipulate phylogenetic trees.
Here is step by step tutorial on comparing structures and sequences with MultiSeq.

Here you can find original publications for both VMD and MultiSeq:
VMD:

Humphrey, W., Dalke, A. and Schulten, K., VMD - Visual Molecular
  Dynamics., J. Molec. Graphics, 1996, 14:33-38.

MultiSeq:

Roberts, E., Eargle, J., Wright, D. and Luthey-Schulten, Z.,
  MultiSeq: Unifying sequence and structure data for evolutionary
  analysis. BMC Bioinformatics, 2006, 7:382.

I don't think that the problem for OP is the MSA or conservation analysis, it's that the PDBs have incomplete sequences and this will cause issues with python's parsing.

Incomplete sequences is a common problem. One way of getting around it is submitting your PDB ID list to an ID mapper. The one at Uniprot works well. Simply copy and paste your PDB ID codes. Make sure you're going from PDB to UniprotKB (see picture below. Hopefully you'll be able to map most if not all of your IDs.

After you have that, download the text file. Then you can extract the sequences from that text file with the following script:
from Bio import SeqIO
filenames = ["YOURINPUTFILE.txt"]
input_format = "swiss"
output_filename = "YOUROUTPUTFILE.fasta"

output = open(output_filename, "w")
for filename in filenames:
    for record in SeqIO.parse(filename, input_format):
        sequence = record.seq
        output.write(">%s\n%s\n" % (record.id, sequence))

Then submit those sequences to your favourite MSA tool. I answered a question on how to make an MSA here if you've not made one before.
A minor, and perhaps obvious point on reflection, is that the residue number won't be the same in all your sequences due to indels. You will need to reassess this situation when you get there if you still plan on mapping the conserved residues to 3D structures rather than a sequence.

You can use Ensembl (http://www.ensembl.org/index.html) to retrieve orthologues of the protein, and align them using one of many free, web based programs (such as ClusterOmega)


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Density of cells in human tissues?
Where can I find values, or estimates, of the density of cells in human tissues? Maybe an overall estimate, or distinct values for distinct tissues? Or maybe not human, but mammal tissues (which should be similar)?

Good question. I would like to see such estimates as well.

for a comprehensive overview of values, and their sources, please see: http://bionumbers.hms.harvard.edu/search.aspx?log=y&task=searchbytrmorg&trm=density+of+cells&org=

Well, Sender, Fuchs, and Milo wrote a paper to discuss the total number of cells in the body and compare it to the number of bacteria in the body (http://dx.doi.org/10.1101/036103). Their discussion is quite in-depth.
There are a number of ways to calculate it, but an interesting one involved calculating mammalian cell density by a study measuring the DNA obtained from a 25 g mouse. Researchers were able to determine there were 3*109 cells in the mouse (Baserga, 1985). From this study we can simply divide to find a value for "typical" mammalian cell density--1.2*108 cells/g.
If you want to know the number of cells per mL, you'll need the density (g/mL) of the tissue you are measuring. As the comments have mentioned, this is typically around 1 g/mL and varies from person to person. There is a web page that has some tissue densities for various tissues.
Baserga, R. (1985). The Biology of Cell Reproduction (Harvard University Press).

This is close, but not complete. To get from here to cell density, I have to know the weight of a given volume of tissue.

@becko: My wife can drift afloat on water, I can't. I'd say that gives roundabout 1 g/cm^3 for human tissue on average. More for bones, less for fat. ;-)

@DevSolar I updated the answer to reflect your suggestions. Thanks!

The 'cleanest' data I am aware of is on studies using density gradient centrifugation.  In density gradient centrifugation, a preparation of cells is layered on top of a density gradient media which has higher density than water (water=1g/ml).  Centrifugation forces denser cells through the media whereas cells with equal or lower density remain above the solution.   Common values of gradients are 1.084g/ml, 1.077g/ml and 1.073g/ml but a useful overview of the technique can be found here. According to a manual for one density gradient product, Ficoll-Paque PREMIUM (search the GE website), GE Lifesciences says:

Ficoll-Paque PREMIUM 1.073 can be used when isolating lower density
human mononuclear cells, for example mesenchymal stromal/stem cells or
monocytes. The higher density lymphocytes and granulocytes will
sediment through Ficoll-Paque PREMIUM 1.073 to the bottom of the tube,
thereby enriching the lower density cells at the interface.
Ficoll-Paque PREMIUM
1.073 has been found superior to Ficoll-Paque PREMIUM for isolating mesenchymal stem cells from human bone marrow (56).
Ficoll-Paque PREMIUM 1,084 can be used for preparation of cell fractions including
higher density human mononuclear cells or for isolating lymphocytes
that form rosettes with autologous red blood cells (15). It can also
be used for separating blood cells from mice and rats, since the
lymphocytes in rodents have a slightly higher average density than
lymphocytes in humans (50, 51).

If you wanted to try and evaluate density of isolated cells within 'solid' tissues your results would require careful (often enzymatic) release of cells from their integral contact with the extracellular matrix and other cells.   I also presume you could try chunks of tissue.
Density gradient centrifugation can also be performed by layering proportions of gradient media of two densities, resulting in a continuous gradient and more nuanced separation.
TL;DR blood cells are slightly denser than water.

hi guys im new here and i was reading this and would add my own believs to this. and most wont follow this, but... Density is a meassure of complexity. Density equals energy + information. Based on our human build up its only logical our body density is close to that of water but with natural selection law of living things and the reproducing factor of non living things such as stars and galaxy's, i have come to conclude that the thing to understand behind it all is that there is that process, that something that drives energy or matter to change into something else, energy(or equal in matter) + information, that something is the next wheel in our understanding.

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Normal cell diffusion in normal organism?
We know, that cancer cell can travel across an organism.
Is this ABSOLUTELY impossible for NORMAL cells?
For example, is it EXACTLY ZERO probability to find some bone cells inside liver or some skin cells inside brain?
In non-living things and with molecules this is called "diffusion". Any two contacting things will penetrate inside each other after hundreds and thousands years.
Is something similar happening in living thing?
May be very slow?
Was this phenomenon searched for?
Are there some protection mechanisms against appearing wrong tissue cells inside another tissues?
I understand that cells appear in their places during grow, but in mature state I think it is not impossible for cells to travel.
UPDATE
I know that there are many cells that travel by nature, like blood cells.
The question is namely about "static" cells, those ones we normally regard as non-travelling.
Also, I understand that there are some mechanisms, making cells to prefer their normal places when they divide and grow.
But the question is what about all these mechanisms failed? And how often it happens?
For example, I am 40 y.o. So, how many bone cells from my legs are currently in my brains? Zero? One? Million?

hemotocyte (blood cell) travels quite a bit around the body. Lymphocyte cells go pretty. Lymphocyte (involved in immune system) can go in many different tissues. Does it answer your question?

Depends on your definition of "normal," probably. There are non-cancerous diseases, like endometriosis, which involve cells ending up in the wrong place.

Also, this is a potentially very difficult question because cell "type" is not as well-defined as you would like it to be. It is difficult to tell if a cell is in the wrong place ("ectopic") or just a strange variant of a normal cell type.

In a healthy body, cells travel.
But this is very dependent of the cell type. Some cell type will travel in all the body (lymphocytes, plasmocytes, etc) while other do not have any migration capability.
The concept of diffusion is wrong to apply here, indeed the scales at which you are looking are not molecular.
Moreover, there are very active mechanism to keep cell type in place, for example, a concept called preferential attachment will maintain the cells grouped by cell type. If you take two balls A and B and A attached more to A and B to B, and you shake, you will see appearance of clusters of A and clusters of B. But that is only one such mechanism and a lot of other take play here.
see this: http://www.ncbi.nlm.nih.gov/books/NBK26937/
Thus, the probability of finding a cell type NOT at its normal position (that is one that does not travel) is maybe not zero, but so close to it that you will not find a cell outside of their normal position.
I hope this answers your question ?
Reference
Cooper GM. The Cell: A Molecular Approach. 2nd ed. Sunderland (MA): Sinauer Associates; 2000

Looking at it on my desk, I can't really find a chapter on this, it is too broad a question, it encompasses things from caderine adhesion, to Blood brain barrier.
The most relevant thing I found to this question is probably this:
http://www.ncbi.nlm.nih.gov/books/NBK26937/

Agreed on that. It's very broad. Good attempt though. +1d already :)

The preferential attachment mechanism can't be 100% accurate as anything in nature. Even the very term "preferential" implies uncertainty, because it would called "exclusive attachment" otherwise.

So, the question is namely about cell types we normally regard as non-travelling. For example, can we find bone cell in brain or skin cell in eye? I agree that probability is not zero, but the question is how large is this probability?

The concept of diffusion is actually very relevant - it's one aspect of how you would model the motion of a single cell!


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How does protein enter bloodstream?
If a hemophiliac patient injects his factor 8 through the veins directly into the bloodstream to provide the body with clotting factor... Why don't they just make the drug as a pill and have the liver do its job with extracting protein and dumping it into the bloodstream?

Likely a question for Health SE. But 'proteins do not survive the digest tract all that well' is the likely answer.

Why is that so?

Proteins will be digested through a number of proteases in the stomach and intestines (pepsin, trypsin, etc) into their constituent amino acids. The amino acids are then absorbed in the small intestine. So any specific proteins you try to put into a pill will be digested into amino acids before being absorbed. If you somehow manage to defeat the digestive enzymes, the protein will simply pass through the digestive tract without being absorbed--the intestines don't have the capability to allow larger polypeptides through.
If you think about it, this is probably a good thing. We don't want random proteins from our food running around in our bodies. It would likely kill us in short order.

Welcome to Bio. Nice answer,  but some references to allow for background reading are recommended


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What niche was humanity theorized to fill before we possesd weapons and coordination to hunt & kill large prey?
I'm really interested in evolution, and for a err 'hobbyist' I think I understand a good bit of evolution and adaptation and the role it has played in many species.
However, I feel I'm rather ignorant about a key period of time in human evolution.  When I try to research it (and I have!) I see discussion of humans-as-ape, right around the time we split off from the bonobo & chimp common ancestor, and then discussion seems to skip to the 'cave-man' era of more advanced stone weapons used to take down larger prey animals along with significant coordination.
There seems to be a time gap between these two points, a time when we did not yet have weapons strong enough to deal lethal damage to fleeing prey, and may not have yet had communication skills to arrange complex ambushes.  I'm trying to figure out what evolutionary niche humans possessed prior to having weaponry for killing large prey.  Were they scavengers, mostly dependent on fruits, hunt smaller prey etc?  I really have no image at all of humanity role or how it evolved during the gap prior to being capable of the coordinated hunts.
The only theory I have heard of is the use of persistence hunting to basically chase prey before it died of exhaustion.  I personally am not that big a fan of that particular theory though (ignoring the massive caloric expense per 'hunt' and difficulty of doing it in stone age, prey species would quickly evolve to not run to exhaustion from otherwise non-dangerous humans rather then constantly letting themselves be killed this way if it was the primary hunting strategy of humans).
I realize that this far in time there is no consensus on exactly how humans evolved or exact roles they may have played.  however, I'm hoping someone could point me to some theories or discussion for how pre-weapon human may have lived?

If I understand your question correctly, I think it would be easier and less wordy to indicate a date and ask about the feeding behaviour of humans at that date. I suppose you are interested in maybe 2.6 millions years ago (right before the invention of tools for hunting).

If you want to keep learning about evolutionary biology, then you might want to have a look at an introductory course to evolution. Understanding Evolution (UC Berkeley) is an online free resource.


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Diffusion coefficients of glucose in mammal tissues?
Where can I find estimates/experimental measurements of the diffusion coefficient of glucose in mammal tissues? Specefically I mean the inter-cellular space. I'm not looking for a specific tissue, so some examples of values for some tissues, or a generic estimate, is enough for me.
And the same for lactate, although I presume it will be very similar.

Something to start with! (see table 19.1)

This question cannot be answered as is. What do you mean by tissue ? Inter Cellular space ? Cytoplasm ? Nucleus ? Blood stream ? etc etc All of those media have very different diffusion properties.

@Xqua I mean extracellular glucose, inside a tissue, so it's in the inter cellular space. I edited the question.


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Difference between negative allosteric regulation and non-competitive inhibition
Both connect to some site other than the active site which controls the shape of the active site and causes the enzyme to be less active. So what is the difference?

For allosteric inhibition, the inhibitor binds to the enzyme and induces a change in the conformation so that the substrate cannot bind anymore. The binding site for the allosteric inhibitor is different from the substrate, see the image for illustration (from here):

In non-competetive inhibition the inhibitor also binds to the enzyme indepently of the substrate (wheter it is bound or not) and does not influence substrate binding. What is influenced is the activity of the enzyme, when the inhibitor is bound, it will not process the substrate. See the figure (from here) for illustration:

So in allosteric inhibition what's changing is the affinity to the substrate, and in non-competitive inhibition what's changing is the ability of the enzyme to carry on with the reaction. Got it.

@A.Steiner no. The difference is that in allosteric inhibition, the inhibitor does not bind to the active site but to some other site in the enzyme which, due to change in enzyme structure, leads to change in activity.

@A.Steiner No. In allosteric inhibition the conformation of the enzyme is changed so that the substrate cannot bind anymore. In non-competetive inhibition the substrate binding is not affected.

@WYSIWYG, I pretty much believe that both of them (allosteric/non-competitive) bind to a regulation site which is not the active site, change the enzyme conformation and lead to change in activity.

@Chris, an allosteric regulator changes the conformation of the active site, but with saturation of substrate I know the enzyme suppose to work as there is no regulation at all - changes the affinity to substrate (Km) and not the ability of the enzyme to work (Vmax). in that perspective it's dynamics behave like a competitive inhibitor. In non-competitive inhibition, the enzyme will not work the same no matter how much substrate there is. Meaning the effect is not on affinity, like you said. The enzyme structure must be changed though (CoE/critical amino acids) in order for it not to work.

@A.Steiner a non-competitive inhibitor binds to the active site (not necessarily the substrate binding site); it may or may not change the conformation of the active site. Allosteric term itself implies "other site" and the only way by which an allosteric regulator can affect the activity of the enzyme is by changing the latter's conformation. If you don't want to believe this then I cannot help.

@WYSIWYG this is from Wikipedia - "It is important to note that while all non-competitive inhibitors bind the enzyme at allosteric sites (i.e. locations other than its active site)—not all inhibitors that bind at allosteric sites are non-competitive inhibitors". If it is not the substrate binding site, it is not the active site. Active site - "the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction"

@A.Steiner As a molecular biologist I cannot agree with this Wikipedia article that is not properly referenced. First of all, active site is not just the substrate binding region, it is the region of the holoenzyme which is directly involved in catalysis. A non-competitive inhibitor binds somewhere in the active site (including cofactor) and prevents catalysis. An allosteric regulator (can be an activator too) bind at some other regulatory site. All these definitions are historic. We can extrapolate that allosteric regulators affect enzyme catalysis by causing overall change in structure.

There Are Two Similar but Distinct Types of Noncompetitive Binding.
Starting from a pharmacological perspective, there are 2 definitions of "noncompetitive" binding that have similar macroscopic effects but differ slightly in their molecular mechanisms. Depending on which definition you use, noncompetitive ligands can bind either orthosterically or allosterically. Aspirin at cyclooxygenase and alanine at pyruvate kinase have both been referred to as "noncompetitive" (see below), despite aspirin binding orthosterically and alanine binding allosterically. Both types of inhibition involve depression of the maximum response, efficacy or enzyme activity. In other words, they reduce $y_{\mathrm{max}}$, $E_{\mathrm{max}}$ or $V_{\mathrm{max}}$. This is described in (Lippincott. (2015). Illustrated Reviews Pharmacology. 6th ed. p. 34). Similarly, (Goodman and Gilman. (2011). The Pharmacological Basis of Therapeutics. 12th ed. p. 46) gives an operational definition of noncompetitive antagonism as that which depresses the maximal response to the agonist but the molecular mechanism of action "really cannot be inferred unequivocally from the effect". The two types of noncompetitive molecular mechanisms are (1) irreversible antagonism and (2) allosteric antagonism. Lippincott claims that both of these mechanisms are "noncompetitive" antagonism. Textbooks trump Wikipedia on credibility so I'm afraid to say that Wikipedia may have been leading people astray for years by saying that noncompetitive ligands can only bind allosterically. Due to this confusion, I think it's better to avoid the term noncompetitive entirely and opt for "insurmountable" inhibitor if the mechanism is unknown, or "irreversible/allosteric inhibitor" if the mechanism is.
Type 1: Irreversible Antagonism
Goodman and Gilmans' definition in the previous paragraph notes that the effect is for "a slowly dissociating antagonist" (i.e. an irreversible antagonist). This is mirrored in (Rang and Dale. (2015). Pharmacology. 8th ed. p. 11) and (Katzung. Basic and Clinical Pharmacology 11th ed. p. 31), which define noncompetitive antagonism as irreversible antagonism. Rang and Dale also makes the point that the term is ambiguous with other meanings of noncompetitive. Rang and Dale claim that aspirin is a noncompetitive antagonist at cyclooxygenase. It may be an irreversible antagonist but it's certainly not an allosteric one, as it modifies the orthosteric binding site. Another "noncompetitive" drug in this class (according to Rang and Dale) is phenelzine, which irreversibly binds MAO.
Type 2: Allosteric Antagonism
Not to be confused with negative allosteric modulators, (Goodman and Gilman. p. 46), (Rang and Dale. p. 17), (Lippincott. p. 34) and (Katzung, p. 32) all give a second definition of noncompetitive antagonism as antagonism at an allosteric site. This antagonism may be reversible or not but as the agonist can't displace the antagonist, it is insurmountable in all cases. Rang and Dale give the example of ketamine at the NMDA receptor, which depresses the maximal response by binding in the channel (an allosteric site) but doesn't bind irreversibly. For ligands relevant to enzymes, alanine and ATP allosterically (yet reversibly) bind pyruvate kinase. So this would cause insurmountable inhibition of pyruvate kinase activity but not irreversible inhibition. Various authors, such as (Mustafa and Hochachka, 1970) refer to this as "noncompetitive" inhibition.
Interestingly, I can't find any exogenous ligand that is both reversible and allosteric. It seems that allosteric antagonists are more relevant to receptors and transporters than enzymes. To make it even more confusing, Katzung claims that benzodiazepines (BDZ) act noncompetitively, since they bind allosterically. But this doesn't fit with any other definition of noncompetitive binding since BDZ is a positive modulator. Also interesting is that hexamethonium at the nAChR fits the definition of "noncompetitive", regardless of which one you use. It is an irreversible blocker at an allosteric site.
Marangoni, on p. 70 of Enzyme Kinetics: A Modern Approach, also points out the difficulty in distinguishing between irreversible orthosteric and reversible allosteric inhibition. Using an irreversible inhibitor is equivalent to removing some enzyme from the system, so $V_{\mathrm{max}}$ drops. But at the same time, an allosteric inhibitor causes insurmountable inhibition (reduces $V_{\mathrm{max}}$). Neither type of inhibition alters the affinity of the substrate for the active site of the enzyme (apart from the irreversibly inhibited enzymes with no affinity) so $K_m$ is left unchanged. The figure below, from (Jahangirvand et al., 2016), shows the antagonism of catalase by cimetidine on a Lineweaver Burke Plot. A glance at this graph tells us that $V_{\mathrm{max}}$ is depressed, while $K_m$ is unchanged, so we could (arguably) call this noncompetitive inhibition. But this would not tell us the molecular mechanism of the inhibition.

This is a well written and researched answer. Thanks comments are discouraged but this answer deserves credit!

Anyone reading this article should note that the IUPHAR published a standardisation of terminology which settles the dispute. I'll change my answer in due course.


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How do animals with fur get enough sunlight to produce vitamin-D?
How is vitamin D synthesized in animals with fur; how do the cells get enough sunlight? If vitamin-D cannot be synthesized because of limited sunlight reaching the skin, do these animals have to obtain the vitamin from the diet or are there any alternate mechanisms of synthesis?


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Which literature/study/myth spurred the idea that urine is sterile?
There is a seemingly unfounded mantra that a person's urine is sterile who is not suffering from a UTI.
So far I have found convincing evidence to the contrary; urine is not sterile. This poster abstract and publication by Hilt et al., 2014 shows that urine may not be sterile. They list 6 other articles (references 3-8) that also found evidence for microflora in healthy urine, the urethra, and the bladder. In some of those studies males were used, and some used females. This makes a convincing case for non-sterile urine.
But why does this mantra persist; where does it come from? Is there a paper that demonstrates the sterility of urine that I have missed? Even if it is old literature, or pop culture, I'd appreciate it.

You answered your own question. Hilt et al's paper and others have had more than convincing evidence that urine is not sterile. As to why this idea persists? Overall, because of ignorance: either people don't put in the effort to learn real facts or (in the case of other biologists) they don't keep up with the literature. You also can't ask any biologist (e.g., a cell biologist or ecologist) if they believe urine is sterile and believe they know much (any) more than a non-biologist

As there definitely are uropathogens, you can at least be sure urine is not always sterile. I have heard people talking about obligate pathogens in the urine and they definitely found microflora in healthy urine. But that was personal communication (and as far as I know the group studying their own urine because they needed to know whats there before using it to grow other bacteria, so not a study setting to be published).

I think the main point about the sterility myth is that is around for a long time. And it took the group, which finally found the bacteria quite a while to proof this. So to this point nobody was able to find bacteria, thus is was declared sterile. We could have know better, since we are populated with bacteria.

In a healthy person urine is sterile up until the point it leaves the bladder through the urethra. At least, that's what I thought. It depends on where in the system you are looking at it. After it leaves the kidneys it must be sterile.

@Christiaan According to the citations I found there are bacteria in women's bladders[1, 2]. Men are somewhat less studied since UTIs are far less common. Sorry to be a party pooper, but I'm after a reference that supports your statement.

@James - Just sharing what I know - nothing to be pooped. That's why I comment only. Won't go for an answer as it's not my expertise.

@Christiaan My last comment came across quite aggressive, apologies! I thought sterile bladder urine was the de-facto case too until these papers were pointed out to me, but I can't find anything (peer reviewed) to support urine sterility.

It's a good question. +1

But why does this mantra persist; where does it come from?

Behind this line of inquiry is a fascinating observation about the disconnect between the laboratory and the clinic. The basic answer, from my perspective, goes like this:

It is doctors who talk with people about their urine, and any testing thereof;
for doctors, urine is practically1 sterile; and
among those who are aware of the microbiologic reality, doctors inevitably gloss details when explaining laboratory results to patients.

The average clinician learns most of what he knows about his patients' urine from urinalyses. Most clinical urinalysis assays show negative nitrites and negative leukocyte esterase in normal people. A glance at the reference ranges for a clinical assay will demonstrate this. (See also the clinical review below.)
Ideally, urinalyses should not be performed in patients without relevant symptoms, but they are sent anyway, and they're mostly negative.2  Even in people who have symptoms possibly suggesting a UTI they're frequently negative.  Furthermore, urine cultures from properly collected specimens grown on the media used in clinical laboratories mostly return at 72 hours: "no growth". This point is emphasized in the abstract by Hilt et. al. linked in the question. Of the cultures that grew in their "expanded quantitative urine culture" protocol,

90% of these specimens were deemed "No Growth" by the standard urine culture technique, highlighting its limitations.

The last phrase "highlighting its limitations" is an interesting one. It appears to me to be yet to be proven that this is a clinically meaningful "limitation" of such assays. Without attempting to refute these data  — fortunately this question doesn't require me to do so — I will note that the two linked studies aimed to show that people with overactive bladder are characterized by increased urinary flora. The explicitly stated hypothesis is that this may contribute to symptoms. Even in this study demonstrating the existence of such a micro-biome even in normal people, then, it is understood as a potentially pathologic state.
The reason this "mantra persists", then, is that it remains true for clinical purposes. In contrast to most (all?) other bodily discharges, urine is not packed with bacteria, and the commonly used assays reflect this fact.  Medicine and laboratory science have different "modes of discourse", each calibrated to convey levels of precision that are appropriate to the outcomes of interest.

Notes

1. In American English at least, that adverb is ambiguous, meaning either "for practical purposes" or (idiomatically) "almost". Both senses are intended here.

2. Of course, there are plenty of data in various populations demonstrating that some substantial minority of urinalyses among asymptomatic people return positive, "proving" that we shouldn't be checking them (amen!). But this is not the point. The gestalt remains: normal = negative.

3. The nitrite parameter in particular is not especially sensitive. It is, however, quite specific (92-100%), meaning it reliably returns negative in people without infection. (See review, below.) Of course, negative nitrites does not mean sterile in the sense that the OP has used it; see "modes of discourse", above.

Reference

Simerville JA, et al. Urinalysis: A Comprehensive Review. Am Fam Physician. 2005 Mar;71(6):1153-1162.

Really great, satisfying, answer.


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Difference between LH and ICSH
Are Luteinizing hormone and Interstitial Cell Stimulating Hormone(ICSH) the same?

As far as online dictionaries (Medical Dictionary, Merriam-Webster) and a popular-scientific site on hormones (Your Hormones) go, LH and ICSH are the same. ICSH mainly pops up in the older literature; e.g., Lostron & Johnson (1966) and Louvet et al. (1975). My understanding is that LH is currently the more accepted term for the hormone.
I get the impression that historically, LH has been used in relation to female reproduction and ICSH to the male reproductive systems. In males, LH stimulates Leydig cells in the testes to produce testosterone. In females it stimulates the ovarian follicles to produce oestradiol, and it induces ovulation.
References
- Lostron & Johnson, Endocrinology (1966); 79: 991
- Louvet et al. Endocrinology (1975); 96(5): 1179-86


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Difference between DNA and Genome
Can we safely use the terms DNA and Genome interchangeably or is there any (even slight) difference between the two?

note that epigenetic aspects are essential to body plan embryo morphology yet are not considered part of the Genome, due in part to current limitations of DNA sequencing

@ScottStensland I learnt the meaning of your comment now after attending Epigenetics course. Thanks Scott!

Oversimplifying:

DNA is a specific form of molecule (desoxyribonucleic acid).
Genome is the information of a specific organism stored on its DNA. (Not just his genes, i.e. the information in the coding parts of his chromosomes, but the whole of it.)

With just a little bit of scientific handwaving, you could conceivably synthesise DNA molecules that are just random sequences of ATCG. It wouldn't be the genome of anything.

I'd add that retroviruses have a genome not encoded by DNA, but RNA; and PCR primers are DNA not encoding a genome.

DNA is any piece of DNA. Genome is a very specific piece (or pieces) of DNA: all of the DNA contained inside one cell, or organelle, or virus particle, from a specific species.
For a species with a single chromosome, like the bacterium, E. coli, then the bacterial genome is equivalent to the cell's chromosome. Same for a virus. For a metazoan, like C. elegans, which has six chromosomes, the nuclear genome is one copy of all the chromosomes and the mitochondrial genome is one copy of the mitochondrial chromosome.
So DNA is a general term, while genome is a specific term that can be used most clearly with a modifier to specify the species you are referring to (e.g., the human genome, or the duckbill platypus genome, etc.).