How can action potentials be generated through thoughts? I think I understand how a signal is transferred from neuron to neuron (from  How do the brain and nerves create electrical pulses?).

My question, however, is not about the standard textbook material on neuronal transduction. Instead, I am wondering how an electrical impulse starts in the first place in the brain. In other words, how can an action potential be generated de novo from a conscious thought? I am wondering primarily about a signal like a movement of an appendage or something similar.

So in short, my question is:

How is the 'first' action potential generated in the cortex when one consciously/voluntarily decides of moving a limb (or comparable action)?

This paper addresses the question that you are asking. The study is based on conscious decision making in rats.

Performance of rats were assessed in the following task:

The rats have to poke their snout into a waiting port until a auditory signal (beep) is heard.
After first beep the rats can get a small reward (small amount of water) in the reward port. However if the rat waits for a second beep it gets to have a bigger reward.

So there were three behavioral outcomes in the experiment done with 37 individuals:

Short-poke trials: Those that didn't wait for the signal (8.3 ± 4.6%)
Impatient trials: Those that waited for the first beep but did not wait for the second beep (58.8 ± 3.9%)
Patient trials: Those who successfully got the bigger reward. (32.9 ± 1.4%)

The impatient ones did not usually quit immediately after the first beep. This was not a lethargic response to signal but a moment of conflict between two decisions. There was a distribution of waiting times. The patient ones immediately responded to the second beep and took their reward.

Neural activity was studied in the M2 (secondary motor) cortex of impatient rats during the tasks and two kinds of neural activity was observed:

Ramp-to-threshold: Firing rate kept increasing till the end of waiting time suggestive of a neural threshold to quit waiting. (Fig 1)
Steady-transient activity: Firing rate correlated with waiting time i.e. higher firing rate higher the waiting time. This could constitute the neurons that are making the rat wait. (Fig 2)

  Figure 1: Ramp-to-Threshold.  Reproduced from Murakami et al. (2014) Nature Neuroscience 17,1574–1582

  Figure 2: Transient activity.  Reproduced from Murakami et al. (2014) Nature Neuroscience 17,1574–1582

It was also observed that this activity is task specific. The neurons that showed a certain activity in the above tasks did not behave the same way in the same rats performing a slightly different task.

So action potential is generated in the brain by "thoughts". However these thoughts are not generated de-novo. Any conscious decision is based on memory of past events and similar events evoke those memories, which in cellular terms is generation of action potential. In this case the action potential is generated in response to the rats' sensory input in the form of a beep. Other kinds of responses are instinctive and the brain circuitry has evolved to generate these kinds of responses to certain stimuli such as fear. The above example is a study of conscious decision making based on an acquired memory.


M-type potassium channels by muscarinic receptors How does the closure of M-type potassium channels by muscarinic receptors result in increased excitation of the target neuron?

Closing of the channel through muscarinic receptors involves activation of phospoholipase C and depletion of membrane phosphatidyilinositol-4,5-bisphospate which is needed for the channel to stay open. Once the channel is closed,  potassium, which is a positive ion accumulates inside the cell eventually depolarizing it or lowering its threshold for activation. Thus, blocking the extrusion of K ions results in excitation of the target neuron.

See this for more:
Brown, D. A., and Constanti, A. (1980). Intracellular observations on the effects of muscarinic agonists on rat sympathetic neurones. Br. J. Pharmacol. 70, 593–608.


How exactly is glyceraldehyde 3-Phosphate reverted to ribulose 1,5-bisphosphate for the continuation of the calvin cycle? Around 6 molecules of G3P is produced at the end of the Calvin Cycle (light independent reactions of photosynthesis), and 5 of which are reverted back to RuBp.

The general equation that I read is 5 G3P -----> 3 RuBp using 3 ATP.

It however doesn't seem to add up (regarding balancing of the atoms) as 5 phosphates would be converted to 6.

I would appreciate a link to any resource explaining this process in detail.

Thank you and have a nice day ^^

You need to account for free phosphates (Pi) that derive from ATP and are released in phosphatase reactions. The regeneration of 3 ribulose-1,5-2P has the overall reaction

5 glyceraldehyde-3P + 3 ATP $\rightarrow$ 3 ribulose-1,5-2P + 3 ADP + 2 Pi

So in total eight phosphates (here counting ATP as 1) are redistributed, 6 of which end up in ribulose-1,5-2P, and two are released as free phosphates. (These Pi are then recaptured during ATP synthesis in the light-dependent reactions.)

The above is a summary reaction of course; the complete scheme involves 10 enzymatic reactions that rearrange carbons in various ways to form 5-carbon sugars from 3-carbon ones (which takes a bit of juggling of atoms). Release of free Pi occurs in the fructose biphosphatase and seduheptulose biphosphatase steps.

A detailed account can be found in any major biochemistry textbook, like Stryer's Biochemistry. Online resources like MetaCyc can also be helpful.


Why cold water results in cough I have a pretty simple question which always kept me intriguing since childhood and I couldn't find its precise answer yet. Why do we cough by cold water. Recently I had flu and found very strange correlation between cold water and coughing. Even seconds after drinking cold[er] water, I started coughing as you all would have experienced as well. So why does it happen?

I am no expert in this but I had asked my doctor the same question the last time I fell sick and I'll try to paraphrase his explanation.
"There is this protective lining on our respiratory tract called "Respiratory Mucosa" that acts as the first line of defense against pathogens. But when you consume cold food and beverages , this membrane gets congested or shrinks such that it exposes the respiratory tract to pathogens . This is more prevalent if your body has an elevated temperature such as after spending a lot time outdoors during summer or after a workout. Cold food as such doesn't make you sick but they make it easier for the pathogens."
A quick Google search turned up this
http://www.thehealthsite.com/diseases-conditions/why-does-drinking-chilled-beverages-cause-sore-throat/#
Your cough could be a symptom of having a sore throat from infection.


Consequence of touching Formaldehyde I accidently touched formaldehyde some days ago. Skin on my hand got dehydrated as if I had placed it in salt solution. I washed it with water and it returned to normal state after 5 minutes.
But now whenever I wash my hands with water my skin gets dehydrated again, but returns to normal state after some time .
What's the reason behind it getting dehydrated again when exposed to water ? Will it return to normal state when new skin grows back ?
By dehydration, I mean something like this.

cool pics!

Firstly, Formadahyde is a terribly toxic substance.

  Skin Contact: CORROSIVE. Contact can cause pain, redness, burns, and blistering. Permanent scarring can result. Can be absorbed through the skin.

Formaldehyde causes organ failure and scarring if ingested.

In this case, since you don't have burning or blistering, it seems like a reasonably low exposure. You should nonetheless call your doctor to check in or drop by the campus infirmary or what you have.

A good experience to remind you to wear gloves when working with chemically active reagents or solvents (DMSO for instance!)

I'm not a doctor, but as a non professional and informal opinion, your finger will probably become normal again, eventually all the cells will do their best to repair themselves.


Can cell exist without Ribosomes? Last night I came across a question that goes as follows:-

Cells cannot exist without
a) cell wall
b) cell membrane
c) mitochondria
d) ribosomes

I am getting confused with option B and option D

If RBC is lacking ribosomes then where the antigen proteins on RBC are coming from ?

The most essential thing for a cell to survive is a membrane. Without a membrane there is no boundary between cell and its surroundings. A selectively permeable membrane is needed for cells (from single celled organisms to elephants and giraffes and whales) to survive. Cells will die quickly on removal of cell membrane.

The RBCs are good example of cells without mitochondria or ribosomes which survive for 120 days.

Please read the article on Erythropoiesis for detailed information on how RBCs form and how they have proteins in their surface.

In short, the RBCs acquire the surface proteins during their formation period in the bone marrow. Inside the bone marrow the premature RBCs have nucleus, ribosomes, mitochondria, etc... and produce all the required structural and functional proteins. On maturing they loose the nucleus and cell organelles and contain only hemoglobin in their cytoplasm.


Using cell concentration I am doing an experiment in which I plate for example 3x10^5 cells, and every day I have to count the cells growing. I find the number and a convert it in x10^5. In my graphs I have to use the cell concentration. I am not sure which units are used for cell concentration. Is it ml, μl or anything else?

What is a concentration

A concentration of cells is the number of cells per unit of volume.

You are free to choose the units you like

It is very much up to you to chose the units you want as long as they express a concentration. There is no right or wrong.

You can express your graph in cells per liter or in 100,000 cells per $\mu$l or in billions of cells per ml, all would be correct. Of course, some are more intuitive than others. I would advice you to avoid expressing in cell per square meter or in billions of cells be nanoliter because the numbers will be very small and very large respectively and will not convey much intuition.

A good intuitive unit

I don't know what kind of concentration you have in you data but a priori, I would recommend expressing your concentration in cells/ml is quite intuitive.


What is the difference between monoecious and homothallic? In my plant reproduction book there are two distinct definitions for these two terms, but when I read them I found out that they are very much alike that I was confused and couldn't catch the difference between them. I searched on Google and found this on wikidiff:

  As adjectives the difference between homothallic and monoecious is
  that homothallic is (of some algae and fungi) producing male and
  female reproductive structures in the same plant while monoecious is
  (botany) that has male and female reproductive organs on the same
  individual plant (rather than on separate individuals).

But, still, isn't this the same sentence using another words?
Thanks for answering.

The difference is that they come from different scientific traditions and describe the same idea for different kinds of organisms. Homothallic is applied to fungi and algae, whilst monoecious is applied to plants (and sometimes invertebrates). This use of different words to describe the same phenomena in different types of organisms is unfortunately quite common. You could also had hermaphrodite as another example for organisms with both male and female reproductive parts. One can point to crude phenotypic differences to justify the distinction in terms but the underlying concepts are the same.

I note as well that the separation into different types of organism used is usually based on older classification systems rather than reflecting any biological reality.


Master Catalog of all Fossils / Literal Fossil Record? Is there a website or other resource that catalogs all fossils ever found? Basically, is there a literal "Fossil Record"?

Where do scientists gather their results from excavations? Are they just scattered in various peer-reviewed papers in science journals?

I'm imagining something like manuscripts and master texts. You have some researchers who analyze manuscripts to produce the text of that manuscript in electronic form, for instance. Then, other researchers take these various readings and assemble a master text, taking into account the variations and attempting to recover the original work.

By analogy, this would be like when a paleontologist at a dig site submits a paper about his/her findings to a science journal. Is there another group of scientists who look at all of these papers and compile a "master text" of the fossil record?

fossilworks.org and paleobiodb.org are reasonably good databases for fossil records. Paleobiodb has even got a map based view which is really convenient. Thank you.


What happens in a brain of a person suffering with apathy? According to this article

  Apathy is a profound loss of motivation not attributed to decreased
  level of consciousness, cognitive impairment, or emotional distress.
  Apathy refers to a set of behavioral, emotional, and cognitive
  features such reduced interest and participation of activities of
  daily life. Another prime characteristic is lack of initiative or an
  absence of responsiveness to stimuli as demonstrated by a lack of self
  initiated action.

Could you describe what happens in a brain (on the level
of neuroreceptors) of a person suffering with a lack of
motivation (or apathy)? And how does it look in the healthy
brain?

Starting your comment, first, apathy in itself is not a disease; it's not categorized as such by any medical or psychiatric organization. It is part of the symptoms of some disorders, including depression, schizophrenia and Alzheimer's.

Furthermore, apathy is not a simple symptom, but rather a constellation. That also makes it more difficult to address its brain correlates. From a review,  Moretti & Signori (2016):

  Apathy is an uncertain nosographical entity, which includes reduced motivation, abulia, decreased empathy, and lack of emotional involvement; it is an important and heavy-burden clinical condition which strongly impacts in everyday life events, affects the common daily living abilities, reduced the inner goal directed behavior, and gives the heaviest burden on caregivers. Is a quite common comorbidity of many neurological disease. [...] As a general observation, the occurrence of apathy is connected to damage of prefrontal cortex (PFC) and basal ganglia; “emotional affective” apathy may be related to the orbitomedial PFC and ventral striatum; “cognitive apathy” may be associated with dysfunction of lateral PFC and dorsal caudate nuclei; deficit of “autoactivation” may be due to bilateral lesions of the internal portion of globus pallidus, bilateral paramedian thalamic lesions, or the dorsomedial portion of PFC. On the other hand, apathy severity has been connected to neurofibrillary tangles density in the anterior cingulate gyrus and to gray matter atrophy in the anterior cingulate (ACC) and in the left medial frontal cortex, confirmed by functional imaging studies. These neural networks are linked to projects, judjing and planning, execution and selection common actions, and through the basolateral amygdala and nucleus accumbens projects to the frontostriatal and to the dorsolateral prefrontal cortex. Therefore, an alteration of these circuitry caused a lack of insight, a reduction of decision-making strategies, and a reduced speedness in action decision, major responsible for apathy. Emergent role concerns also the parietal cortex, with its direct action motivation control.


Why does the "all-or-none" principle hold true for only single nerve cell, and not a bunch of nerve cells? I've read this from wikipedia:

  ... This relationship holds only for the unit of tissue; for nervous tissue the unit is the nerve cell, for skeletal muscle the unit is the individual muscle fiber and for the heart the unit is the entire auricles or the entire ventricles.

https://en.wikipedia.org/wiki/All-or-none_law

I know about all-or-none principle but i don't understand this statement. What it is trying to imply? I am not sure my question title is reasonable because of my less understanding.

The "all-or-none" principle refers to the roughly accurate concept that neurons fire all-or-none action potentials, individual muscle fibers contract fully or not at all, etc.

If you have a population of, for example, 5 neurons, the population response is no longer all or none, even if the individual units follow the principle. You could have 0, 1, 2, 3, 4, or 5 cells firing an action potential together (the definition of "together" is somewhat vague; depending on the location/function of a neuron you could consider spikes within 1 ms to be synchronous or you could consider spikes within 100 ms to be synchronous, for example). The more units you have, whether they are neurons, muscle fibers, etc, the more "smooth" the possible outputs are.

The reasons for different numbers of cells being recruited could be differences in thresholds, but it could also be from different inputs to each of the units, different firing histories of each of the units, etc. This arrangement allows for more "analog" responses both within the nervous system and at muscles, because the strength of a signal or the strength of a contraction can be regulated by how many neurons participate, or how many muscle fibers are contracted.

One everyday example of the importance of this system is your grip intensity when holding an object. If your grip was all-or-none, you would not be able to handle a disposable coffee cup without crushing it. By using a population response rather than a single neuron connected to all the fibers in a single muscle, the nervous system can control the strength of a muscle contraction. The same principle applies within the CNS, where population activity can encode seemingly continuous representations of features like colors, frequencies, sizes, etc, despite an underlying code that is all-or-none at the single unit level.


How can i confirm that the given pedigree chart is of an autosomal dominant trait? This image is from the NCERT textbook. In diagram A, which represents an autosomal dominant trait, I found out that autosomal recessive inheritance also satisfies the pedigree. Yet, the NCERT text book states that it is a dominant trait. How can that be? Is it because the dominant trait is more probable here? If so, how is that it is more probable in this case?

Sure, both are possible here!

Your book probably makes an implicit assumption of low frequency for the "red allele".

Assuming, "red" means "disease", it is quite standard to assume that the "red allele" is at low frequency in the population. If this is the case, then it is unlikely that partners of the members of the main family being represented in the tree carry this allele. It is therefore quite standard to assume that partners does not carry the "red allele". If this assumption is made, then recessive autosomal cannot explain the observed tree.


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

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


What is this green micro-organism found living in water? I study biology in France and experiment on water filtration with plants. I found that some chlorophyll-containing micro-organisms (about 10 micrometers in length) were raised in my basin.

I can't decide if this is a eukaryote (it looks like there are cellular compartments) or a prokaryote (it's very small!). I thought it could also be a cyanobacterium, that combines features of both prokaryotes and eukaryotes. Any ideas what this is?

I can't decide if it's a eukaryote or a prokaryote.

Well, that's certainly an eukaryote. We can clearly see the nuclei in the cells of your fist picture, as well as in the cells of your second one (not so clearly, though):

In the image above, the arrow starts right on one of the nucleus of that group of (apparently) three cells.

Besides that, despite some cyanobacteria being very long, 10µm is a lot for a prokaryote. The mean size of cyanobacteria is way less than that.

By the way, this:

  ... a prokaryote or a cyanobacteria (that can combine both characteristics)

Doesn't make much sense, because cyanobacteria are prokaryotes. More precisely, they are Eubacteria prokaryotes.

Finally, what eukaryoyte is this? I can't tell. It's most probably a kind of Chlorophyta, but I'm not able to go to the Class level. If you're interested in identifying it, you can try a taxonomic key. This one is for British freshwater algal flora, I don't know how different French algae are from the british ones: The Freshwater Algal Flora of the British Isles: An Identification Guide to Freshwater and Terrestrial Algae.

If I'd guess (and this is a wild guess), I'd say that this is a Chlorellales, as the famous Chlorella:

Also, have in mind that saying "that's an alga" doesn't help as well: worse than paraphyletic, algae  is a polyphyletic group and, in biology, polyphyletic groups mean almost nothing.


How to incorporate intraspecific variation in discrete characters in comparative analyzes? I'd like to run a multivariate analysis (Pavoine et al. 2011) that aims to disentagle the effect of environmental gradients on traits, considering its autocorrelation with phylogeny and space. It uses the RLQ approach and works with both discrete and continuous traits. However, I don't know how to incorporate intraspecific variation in discrete traits.
For example, I recorded categories of pigmentation on organs of several amphibians, but for some species, these categories vary among individuals. One way would be including individuals as polytomies at the species level, but this would make the test quite hard to interpret.

Thank you in advance,
Diogo

Kostikova et al. 2016. Syst. Biol. developed an algorithm to model trait evolution with inter- and intraspecific variation. The authors use it to show

  whether a life-history trait (i.e. annual versus perennial) influences the evolution of intraspecific variation in the climatic niches of species

While they do not directly incorporate the space component as in the RLQ analysis, the approach might be informative in your case. The functions are available through dryad.


Ancient DNA of ancestors or existing species? Ancient DNA appears to be at most "several hundred thousand years" old.

Do we have an aDNA sample which we can reasonably confidently attribute to a species which has at least two modern descendants?

PS. This question is much less interesting than I originally thought: there are modern species which are proven ancestors of other multiple modern species (lake Victoria Cichlids).

Assuming you mean by "modern descendants" "two different species that are also different from the ancient DNA", then to the best of my knowledge, no; the large vertebrates (bear, horse, humans, mammoths) that have been focused on for the most ancient DNA samples have common ancestors that are outside the range of ancient DNA isolation. I'm not very familiar with plant ancient DNA; maize DNA from a few thousand years ago is the oldest I'm aware of, but I might easily have missed some.

However, it's important to point out that the way this question is phrased makes it merely trivia, with no scientific significance.

Assuming (from the poster's other questions) that he believes this is somehow relevant to questions about speciation, I would point to modern genomes from ongoing speciation.  For example, Heliconius butterflies are speciating, and there's some work looking at the genomic components of that speciation:

Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies.
Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing.
Divergence with gene flow across a speciation continuum of Heliconius butterflies

Stickleback fish also show a number of examples of incipient evolution, and again genome studies have been done:

(Genomic landscape of early ecological speciation initiated by selection on nuptial colour.](http://onlinelibrary.wiley.com/doi/10.1111/mec.13774/abstract;jsessionid=DB86FB85259118805B95C1C52138D3EA.f03t03)
Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback.

Since, as I say, the question as phrased is simply asking for scientifically unimportant trivia, I'll leave it that as far as guessing as to what the actual point is.


Why is absorbance at 280 nm for protein solution going up when I measure repeatedly? I have been measuring my protein solutions' concentrations by diluting them in water 20 fold with a final volume of 100 uL and then measuring the absorbances of these solutions in 96 well plates with plate reader. I don't remember having any problem up until today.

I used 20 mM phosphate buffer instead of water to dilute them today and measured the absorbances at 280 nm repeatedly three times and the absorbance for one of the solutions went up from 0.043 to 0.068 (absorbance of 20 mM phosphate buffer is 0.030 at 280 nM with same volume); I stopped measuring after third one but it would probably go higher as I measured until I hit a plateau.

I measured absorbances of two proteins and only one of them went up that much, other one went up from 0.071 to 0.088; if this were to be concentration dependent I would expect the second solution go even higher but it didn't happen.

I know there may be differences in UV absorbances if protein is folded or unfolded; would it be that dramatic? What is the reason for that increase? I will be grateful for an explanation and a practical solution to the problem.

NOTE: I increased the total volume to 200 uL by simply adding 100 uL of 20 mM phosphate buffer into all wells and the signal increase slowed down a lot; there is still some increase though with 0.001-0.003 increments in each measurement.

It looks like your protein concentrations are right on the limit of detection of the spectrophotometer, and changing the diluent buffer changed their concentrations. The samples may not have been thoroughly mixed after dilution and before measurement, so the varying measurements may simply be the solution coming to equilibrium. Temperature can also affect absorbance, so you should verify that your samples have equilibrated before drawing any conclusions. If the absorbance of your phosphate buffer is 0.03, I'd try to keep the sample absorbances above 0.075 or higher to avoid getting too close to the limit of detection. Also, make sure your buffer isn't too old or contaminated with something which could be affecting its absorbance characteristics.

I would suggest taking one or two protein samples and doing a dilution series (1:1, 1:5, 1:10, 1:20) in a large-ish volume (say 400 ul each, if you can spare it), vortex briefly to mix well, then measure triplicates of each dilution on your reader, along with appropriate blanks (buffer only). You will see differences between each measurement, but it should be quite small, depending on the accuracy and precision of your instrument.

Measured values will not be exactly the same from measurement to measurement, and it would take a lot more than three repetitions to determine if there was an actual drift trend occurring. Measure your sample plate every 5 minutes for an hour and plot the values (don't just eyeball them) to see if the machine may need to be serviced.


Plasma Membrane Proteins and Cytoskeletal Attachment Regarding membrane protein functions, which of the following
  statements is CORRECT?

  a. Membrane proteins are responsible for both cell to cell recognition
  and cell anchoring and are stabilised by linking through to the
  microtubulele cytoskeletal ﬁbres.

  b. A protein that is enzymatically active and membrane-bound will
  function significantly differently to a protein that is enzymatically
  active and cytosolic.

  c. Membrane proteins are manufactured in the internal cavity (lumen)
  of the rough ER.

  d. Damage to the smooth ER could alter the makeup of the molecules
  that are displayed at the cell surface.

Regarding membrane proteins, what is incorrect in the statement “Membrane proteins are responsible for both cell to cell recognition and cell anchoring, and are stabilized by linking through to microtubules cytoskeletal fibres"?

I believe this to be wrong due to it normally being Actin Filaments and Intermediate Filaments that attach to Integrin proteins in the cell surface membrane.

a. Membrane proteins are responsible for both cell to cell recognition and cell anchoring and are stabilised by linking through to the microtubulele cytoskeletal ﬁbres.

Not entirely correct as you yourself pointed out that integrins attach to actin filaments.

  b. A protein that is enzymatically active and membrane-bound will function significantly differently to a protein that is enzymatically active and cytosolic.

Possible but not necessary.

  c. Membrane proteins are manufactured in the internal cavity (lumen) of the rough ER.

They are secreted in the ER and modified there too but not manufactured there.

  d. Damage to the smooth ER could alter the makeup of the molecules that are displayed at the cell surface.

Seems correct because the statement itself does not claim certainty. It says that the makeup of cell surface molecules (which could be lipids or proteins) could change in response to SER damage.


What does "local folding" means in secondary structure? I'm new to biology field, so I'm learning all kinds of biochemistry knowledge for a bioinformatics project. I've found a few definitions of secondary structure online. For example, I found this brief definition here:

  A structure of a biological molecule characterized by the local
  folding within the biopolymer as a result of hydrogen bonding (within
  the biopolymer).

What does "local folding" mean here? More specifically, what does "local" in this context refer to? Thanks in advanced.

The most common examples of secondary structure in proteins are alpha helices and beta sheets, and the most important distinction between secondary and tertiary structure is that a single protein can have multiple "local structures", alpha helices and beta sheets, within its complete global structure. In contrast, a protein cannot have multiple "global structures" by definition.

In other words, a local structure can occur multiple times within a protein, while a global structure by definition can only occur once, and describes the complete shape of the protein.


Is a raised baseline between T and QRS normal in any ECG lead? Here are excerpts from an unknown ECG lead. I find it weird that the "baseline" changes after the T wave and doesn't return until after the following QRS complex. Is that normal/expected for any lead?

Click for better resolution. I've got another 10 minutes of the ECG, if that would be helpful.

I am not sure if I understand your question correct. What I can see here is a clear ST depression, that might be indicative of myocardial ischemia/infarction. The underlying mechanism is the shortage of oxygen in myocytes leading to elevation of resting potential and slowing of the depolarization -- this accounts for the elevated baseline after T.

I am not at all an ECG expert, but I have seen the misplaces T-P segment many times while at medical school. It wasn't indicative for diagnosis, whereas all other segments were.

So, why are you worrying about this segment?


Operators and Enhancers/Silencers Wikipedia has two images, of a eukaryotic gene and of a prokaryotic gene.
They show the difference that the prokaryotic gene also has an operator while the eukaryotic gene does not. Both also have enhancers and silencers separately. I thought enhancers and silencers were types of operators. Is this wrong?

Enhancers and silencers are binding sequences for transcriptional activators or repressors, in which case the sequence is often located some distance upstream or downstream of the gene it regulates. See regulation of transcription for information about how these interact with their target genes (through DNA bending, mediator, etc.). A note about enhancers and silencers, though, they're not necessarily required for transcription: they help the gene attain robust up- or down-regulation of transcription.

The operator, on the other hand, influences whether the promoter will do something, or nothing. If we're talking about inducible systems, the repressor is bound to the operator, blocking action to/from the promoter (an inducer will bind the repressor and keep the operator from blocking the promoter). If we're talking about a repressible system, the repressor will need a corepressor to bind the operator to abrogate transcription by blocking action to/from the promoter.


Do hormones make men think of sex? I remember hearing a saying that goes like "men think of sex every 7 minutes (or seconds?)". I take this saying to mean that men have sex related thoughts more often than women.
I'm interested if these thoughts are related to hormone expression within the male body. particularly, I'm interested in the very few seconds before a sexual thought emerges - one moment a man is thinking about daily stuff, next moment his thinking has sexual content. What is responsible for this shift in thinking?
I've read that oxytocin is responsible for men feeling romantic attachment to a partner, but is there a hormone that initiates sexual thoughts or fantasy? For example, would a burst of testosterone increase the likelihood of a man thinking of sex?

Interestingly it does seem as if this is at least in part the case.

Testosterone levels are tied to sexual impulses, but also risky behavior and aggression.  Its responsible for sexual drive in women as well.  Low testosterone can cause depression and loss of the ability to make decisions.

You'll note that the work cited is done on criminals, patients and rats.  Remember that is not medically or scientifically ethical to change the androgen levels of a functioning human being.  Testosterone supplements might increase the chances of prostate cancer.

While its not scientific, there's a fascinating set of interviews about how testosterone affects human thinking at this transcript of American life, Act 2 :

  After testosterone, there was no narrative. There was no language
  whatsoever. It was just, I would see a woman who was attractive or not
  attractive. She might have an attractive quality, nice ankles or
  something, and the rest of her would be fairly unappealing to me.

  But that was enough to basically just flood my mind with aggressive,
  pornographic images, just one after another. It was like being in a
  pornographic movie house in my mind. And I couldn't turn it off. I
  could not turn it off. Everything I looked at, everything I touched,
  turned to sex.


Why do people have antibodies against other blood types? The ABO blood type divides each blood type according to whether they have the "A" and "B" antigen(s) (AB has both, O has none). People also have antibodies against the antigens they don't have (AB has none, O has both), even before they have ever come in contact with those antigens.

Why do people have antibodies against these antigens they have never come in contact with? This isn't the normal situation for the immune system (e.g. for a virus or the blood type rhesus factor)

According to the Wikipedia entry for the ABO blood group system:

  Anti-A antibodies are hypothesized to originate from immune response towards influenza virus, whose epitopes are similar enough to the α-D-N-galactosamine on the A glycoprotein to be able to elicit a cross-reaction. Anti-B antibodies are hypothesized to originate from antibodies produced against Gram-negative bacteria, such as E. coli, cross-reacting with the α-D-galactose on the B glycoprotein.

The cited reference is Van Oss, CJ (2004) Letter to the Editor: "Natural versus Regular Antibodies The Protein Journal 23:357, available here. This source contains this statement:

  ..."we have known for more than four decades that these bloodgroup (antibodies) arise out of minor infections occurring very early in life..."

The cited references are:
Pettenkofer et al. Z. ImmunForsch. 119: 415-429
Springer, GF (1960) Klin. Wschr. 38: 513-514

Unfortunately I have access to neither of these articles, and besides they are presumably written in German.


How are primary monoclonal antibodies for screening mutant cells made, physically? I'm working with a fairly common protein expressed in a large numbers of organisms, let's say a keratin-associated beta-protein. I'm trying to develop a process which requires primary-secondary antibody screening for the keratin-associated beta-protein. Trouble is, it's expensive. Very much so.

I can't find the antibody for any less than $778/mL, and after accounting for dilution and volume required for the recommended protocol, I can't imagine I'll be able to finish designing the process with any less than 20mL. The protein can't change as a design constraint, so there's no reason I'd ever need to change my antibody, but if I need so much... is there any way I can make it myself?

How are these antibodies actually manufactured? Would I need to get ahold of actual B cells and use those, or could I isolate the cellular machinery that produces the antibodies and use that?

Monoclonal antibodies are typically manufactured from a hybridoma cell line. If you are able to obtain hybridomas already made for your antibody (not very likely), or another antibody against your protein, then it's quite easy to produce the antibody yourself. The hybridomas secrete the antibodies into the media, so after growing a bunch of cells, you can purify the antibody from the media with a protein G column.

However, there are not very many hybridoma cell lines available. It's a lengthy and expensive process to make your own (several months and thousands of dollars), even with the help of a core facility/company. You would provide the facility with several milligrams of your protein, they would use it to immunize mice, then after 1-3 rounds of screening, you could obtain hybridoma clones.

There are some banks with hybridomas available for research, for example:

http://dshb.biology.uiowa.edu/

http://www.cellbankaustralia.com/ecacc-hybridoma/


Why use DNA polymerase in making cDNA? RT is capable of synthesizing a complementary dna strand ( as in HIV life cycle.) Then why is
DNA pol used when cDNA (synthesizing the second strand of it ) has to be synthesized from mRNA ( For eg.to construct a cDNA library) ?

Reverse transcriptase, as the name suggests, uses an RNA template to create a DNA transcript (i.e., complement). Once the DNA complement has been made, DNA polymerase is used because it uses a DNA template to produce a DNA complementary strand.

In your specific example, HIV contains a positive-stranded, RNA genome. The HIV RT can use either RNA or DNA templates to produce DNA complements, and this is how the single-stranded RNA genome is transcribed into double-stranded DNA, before integration.

To my knowledge, the RT enzymes sold commercially (for applications like RT-PCR) are typically a mix of an RT enzyme and a DNA polymerase, isolated from other retroviruses, such as murine leukemia virus. An important consideration for lab application is the production of cDNA that truly represents the RNA template of interest. Since RT enzymes typically lack a 3'->5' exonuclease activity, they are unable to "proof-read" the complement strand as it is being produced. In contrast, there are very efficient proof-reading DNA polymerase, and this is why a DNA polymerase (with high proof-reading ability) is used after first-strand synthesis by RT.


Is magnetic resonance microscopy appropriate for investigating ion-channel flow? I've been looking into ways to characterize the elecrophisiology of neurons for cell signaling and I came across magnetic resonance microscopy as a tool for gaining images of neuronal activiy at a large scale.
This made me question, is it possibly to take a timeseries video of an active neuron and view the actual signal flow through and outside of it?

Clarification
I am unclear of your aim. What feature of elecrophisiology do you want to characterize?
What do you mean by large scale? E.g. Micrometers (μm),  Milimeters (mm) or Centimetres (cm).
Magnetic resonance microscopy imagings at Micrometers (μm).
Answer
An established way to observe neuron propagation is the use of calcium imaging. You can take a video under a fluorescent microscope to observe (Not measure) elecrophisiology. Also I believe this technique may provide the 'larger scale' you are seeking.
More On Calcium Imaging:
https://www.cell.com/neuron/comments/S0896-6273(12)00172-9


What does pain look like in wave form? I am interested in understanding what "pain" and "hot/cold" look like, as far as waves signatures (signal processing) go.

My general understanding of how pain (nociceptive pathways) and hot/cold (thermoreceptive pathways) works are as follows:

A sensory receptor (nociceptor for pain and thermoreceptor for temperature) responds to analog stimuli, and synapses an appropriate signal onto a first-order neuron (the neuron it directly connects to); then
The signal travels up the nerve, neuron to neuron, through the spinal cord, up into the brainstem, and finally into the somatosensory cortex; then
That cortex decodes the signal and interprets it as "pain" or "hot/cold"

Further, my understanding is that these signals are electrochemical in nature:

While passing through a neuron (dendrite -> axon) the signal is of a purely electrical form, no different than the electricity racing around the motherboard of my laptop right now; but...
To synapse from the axon of one neuron to the dendrite of the next sequential neuron, the electrical signal is transformed (somehow, this is where I'm fuzzy) into a chemical signal, and essentially hormones/messenger chemicals ferry the preserved signal to the next neuron's dendrite. At that point, the dendrite converts the chemical signal back into electricity, and on and on this goes until we reach the cortex.

So, only because I am a total neophyte here, I have to preface my actual question by asking the greater community at large: is my general understanding here correct? If not, please begin by correcting me!

The question at hand

If everything I've currently stated is more or less correct, then this implies that, while traveling inside a neuron (dendrite -> axon), neurological signals such as pain or temperature exist as waves of electricity.

I'm wondering:

What do these waves look like? Do they have special names? Are they sinusoidal in nature? Do they travel with known periods/frequencies/amplitudes? Can I represent these waves as trigonometric functions?
I'm sure this differs based on genetics and all sorts of other factors, but what are the general power ratings for the central nervous system? How much Watts/Volts/Amps travel with these signals? Are there standard ranges?

Please note: This is not homework! I am a grown man who works as a software engineer by day and I migrated here from the Stack Overflow community. I am asking this question because I have absolutely zero background in biology, and after scouring the internet for an answer to this, I could find nothing.

Please don't hold back with lofty, low-level explanations. Give me science here! Though I am not a biologist, I'm certainly no dummy either.

I don't want to comment about the nature of electric signals in neurons (as I know only little about physiology and neurophysiology). But here is a short answer that may already help you.

Neuronal electric signals are called action potential. If you register the voltage at a given location on the axon of a neuron through time you will see something like this:

This picture shows one action potential. Of course when you feel pain it lasts for more than 5 milliseconds. In such case, if you record the voltage for a longer period of time you will just see a series of action potentials. You should have a look to the wiki page for more information.


Quantity of hemoglobin in the cells According to my book- red blood cells have the ability to concentrate hemoglobin in the cell fluid upto about 34g in each 100 ml of cells.The concentration does not rise above this value because this is the metabolic limit of cell's hemoglobin-forming mechanism.
Furthermore, In normal people,the percentage of hemoglobin is almost always near the maximum In each cell.
The next statement says- the quantity of hemoglobin in each respective cell contains an average of 15g of hemoglobin per 100ml.
So what is the actual concentration of hemoglobin in 100 ml of blood?

The reference range for hemoglobin Hb content in whole blood is 13 - 17 g/100ml for adult men, and 12 - 16 g/100ml for adult women.

There are other related metrics : the mean corpuscular hemoglobin concentration MCHC, that is the concentration in a red blood cell (reference range : 31 - 36 g/100mL), and mean corpuscular hemoglobin MCH, which is mass in one cell (reference range : 29 - 35 pg)

So I think that book is refering to different values :  the concentration in the red blood cell itself (MCHC = 34g/100ml), and the resulting concentration in the whole blood (Hb = 15g/100ml).

By the way, there is a value relating Hb and MCHC, the hematocrit Ht, the proportion of volume of whole blood occupied by red blood cells. Reference range 40% - 50% for adult men, 35% - 47% for adult women.


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?

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.).


Do any fish have to hold their urine in deep water? I know this is going to sound really weird! But I was confronted with this claim and the person strongly had faith in it! I said faith since he couldn't provide any evidence.

Is there any kind of fish that is forced to hold his urine when in deep water ?
If yes, is there any relationship between the case with fish's scale ?
Does that make the fish's meat not proper (poisonous) to eat ?

I don't know what depth would be proper to define here but I guess the matter to be rare and not so important to define.

In a salty environment there is the risk of loosing water by osmosis.
There are different strategies to prevent this.
One of them is to hold the salts of the urine (not the urine itself) by reuptaking them from the kidney.
The resulting high internal salt concentration prevents the water loss.

This strategy is used by Sharks and rays/ skates, they take up urea and TMAO from the kidneys. Those metabolites are highly concentrated in their blood, which makes them unhealthy to eat, when fresh. However, after fermenting they are edible: Hakarl is an icelandic dish of fermented shark. The linked Wikipedia-Article gives more details about the topic.

I guess your friend was referring to this phenomenon, but his memory was a bit imprecise.


Agarose gel Ladder smear We are having trouble with agarose gel electrophoresis. It used to work a couple of months ago but now the ladder always look smeared. We switched the components (1x TBE, 100bp ladder, different type of agarose and voltage) and equipment. We also tried 1.2%, 1%, 1.5% and 2% agarose.

I would appreciate it if someone can help us.

Are you sure that your TBE is at the right dilution? And that you're using TBE to make the gel and also as the buffer for running?  That sort of wavy line looks like what you might get if you'd made the gel with water instead of buffer, or run it with water instead of buffer.  You could also try using TAE to make/run the gel as a sanity check.


How are commercial steroid hormones produced? Does someone know how oestrogens and androgens used for treatment are made? Is it with a GMO bacteria? Is it chemistry?

Thanks

In this recent review you can find fascinating information on all aspects of this topic. It's dense in sterol structures and chemical interconversions, but that's what you have to expect. This is my précis.

Direct isolation from primary biological sources This was the heroic phase of research in this area:

  Androsterone was first isolated from the urine of policemen. Quickly, however, it became evident that natural isolation of hormonal steroids would not satisfy the demand, as, for instance, in 1931, 15,000 L of urine yielded only 15 mg of pure androsterone. Similarly, 4 tons of sows' ovaries were needed to isolate 12 mg of estradiol, while extraction from 625 kg of sows’ ovaries produced 20 mg of progesterone.

[edited by removal of citations]

There are still some commercial processes in this class:
Premarin contains estrogens produced from the urine of pregnant mares.

Chemical transformations starting from steroidal sapogenins of Dioscoreae (yam) These processes still make a contribution but there is a limiting availability of the starting plant material. Apparently important in China.

Direct total synthesis
This section describes chemical routes, but there don't seem to be any commercial processes

Chemical synthesis from cholesterol and phytosterols Phytosterols are plant sterols, available from e.g. soy bean oil, rape seed and paper pulp industrial waste. They can be chemically converted to steroid hormones, as described in the review, but there don't seem to be any commercial processes.

Microbial conversion of phytosterols
Bacteria can convert plant sterols into useful products. Mycobacteria seem to be particularly useful.

  Today, more than 1000 tons of steroids are produced annually from phytosterols by microbial transformation, alone.


Is excessive hydration a risk factor for cancer in humans? I was reading a book on radiation biology, and the book describes the process of "indirect action", where radiation can first ionize a water molecule forming a free radical, which then may interact with important cellular molecules, such as DNA.  This contrasts with "direct action" which involves direct ionization of a key cellular molecule.

The book states that as hydration increases, the probability of indirect action occurring increases.  Given that indirect action normally predominates over direct action in cells, could this mean that over-hydration could be a risk factor for developing cancer in humans? Has there been any research into this?

In addition, would larger humans, who obviously have a larger bodily water content, have an increased risk of developing cancer compared with smaller humans?

In the most technical sense, yes. In a practical sense, no. Average background radiation dose from food and water sources is ~.3 mSv according to the UN. Given that it takes 1 full Sv to increase cancer risk by ~5-6%, it seems unlikely that, under normal conditions, variability in consumption of water will change risk in a significant fashion.

Now, when dealing with highly contaminated water, there may be a more exaggerated effects, scaling with an increased concentration of radioactive particles per unit of water. Of course, in highly radioactive situations the risk of radiation poisoning may be a more immediate worry.


Can breathing in helium (from balloons for example) cause damage to the throat in the long term? Often an activity to do at a party, breath in helium and speak like one of the chipmunks. But, I am wondering, would infrequent inhalation of helium cause long term harm to the throat? in particular, the vocal cords?

When we speak, our vocal cords vibrate to the air. Helium makes them vibrate a lot faster (that's what makes the funny sound of your voice after inhaling helium), because its atoms are a lot lighter than nitrogen and oxygen atoms. Obviously, lighter atoms, can travel faster. This faster vibrations are unusual to the cords and they can cause sore throat or even strong throat ache. After you stop inhaling the gas, things should get back to normal, especially if the inhalation really is infrequent.

Breathing helium balloons at parties is a very dangerous fun activity, because it replaces the oxygen and this could lead to hypoxia - a condition when tissues can't get enough oxygen one reason or another. In some cases, this could even be fatal.

Even though inhaling of pure helium is dangerous, in submarines, divers breathe a mixture of nitrogen, oxygen and helium as helium is better under higher pressures. At these depths the low density of helium is found to considerably reduce the effort of breathing. Divers often have problems with dry throat and constant thirst due to the need of more oxygen. At least, inhaling helium, when it's mixed with oxygen, is far less harmful than breathing it directly from a balloon.


How to conceptualize the action potential? In my AP Biology class, we were taught that action potentials are not electrical impulses in the same way current travels through a wire. Rather, we were taught that action potentials are changing concentration gradients of sodium and potassium ions.

However, when I looked into modeling action potentials I saw capacitances, inductances, and currents--properties associated with electrical circuits.

My question: action potentials--are they electrical currents in the classical sense? If so, what is the charge that is flowing (is sodium and potassium ions?), and how is the overall charge neutrality of the body maintained?

First of all, electric current is defined as movement of charges, $I=\frac{dQ}{dt}$. In electronics that you see around that is not very useful definition, because electrons move much slower than signals, that is changing electric field. Speed of electric field propagation reaches speed of light, whereas electrons move at 1%-30% or $c$.

In biology, especially regarding action potential, only movement of charges is important, not propagation of electric field, probably because conductance is much smaller than in copper wires. that is signal propagates not through interaction between charges, but via intermediate agent/amplifier -- ion channels.

Charge in body is more or less constant, because action potentials are cyclic: after depolarization membrane comes back to -70mV or something. There is no flow of charge out of the body.


How do people digest fat after gall bladder removal surgery? How do people digest fat after gallbladder removal surgery?

How can they tolerate a high fat diet?

This is not a problem, since the gall bladder "only" stores bile, but the production itself happens in the liver. There are some cases described which can get problems digesting very fatty food, but for most people this is not a problem. Additionally eating low-fat food in the first few weeks after the removal is recommended. See here for some more details.

The picture below shows the location of the gall bladder and also the bile ducts (picture from here)


Can you please identify this beetle? Can you please identify this species of beetle? It was about 2 cm (or 0,8 inches) in size. Photo is from Greece, Europe.

The insect in the Photo is a beetle (order Coleoptera), in the scarab family (family Scarabaeidae). It is most likely in the Genus Phyllophaga (June or May bugs) or Phyllopertha (garden chafers).  Beetles such as this are commonly referred to as "Chafers" feeding on plant leaves and flowers during the day. One of the defining characteristics in the photo is the apparent "Hairiness" (setae) visible at the sides of the insect body. I am inclined to agree with the good observations expressed in the comments.  It likely to be a garden chafer Phyllopertha horticola. Some helpful links are below.

https://en.wikipedia.org/wiki/Phyllopertha_horticola

https://en.wikipedia.org/wiki/Phyllophaga

https://www.flickr.com/photos/72271115@N02/galleries/72157651475342046/?rb=1#photo_14184003066

https://www.flickr.com/photos/odonataman/14184003066/in/gallery-72271115@N02-72157651475342046/

https://en.wikipedia.org/wiki/Scarabaeidae


Are genes known or at least conjectured to evolve cyclically ? I observed recently that some people born the same year in not too distant areas (say, in the same country whose size is not too big, like France) share similar phenotypical features, for example they look like each other though they are not of the same family. If confirmed, this would suggest that some alleles are more common within a given period, and hence that the global evolution of the human genetic pool could be statistically determined. One can go one step further and see the considered genetic pool in a given range as a quantum-like system governed by some kind of Schrodinger's equation. I think here of a theoretical framework like Laurent Nottale's scale relativity that could explain these similarities. Have such questions been considered so far?

Welcome to Biology.SE Sylvain!

  I observed recently that some people born the same year in not too distant areas (say, in the same country whose size is not too big, like France) share similar phenotypical features, for example they look like each other though they are not of the same family.

You are likely doing a confirmation or some kind of extended Barnum effect.

You will need to provide a rigorous study for this claim and not just a vague feeling you're having.

  If confirmed, [..]

This piece of sentence suggests that you agree with my previous comments. We expect the OP to provide reference for a claim on which the question lies. One cannot ask "Why do elephants have such a huge genome?" without providing an evidence that they do have a huge genome.

  [..] this would suggest that some alleles are more common within a given period,

If there is such effect it is much more likely caused by shared environment than by shared genetic. Have a look at this post to understand the underlying sources of phenotypic variance.

  and hence that the global evolution of the human genetic pool could be statistically determined.

Sure, it can but this is not a consequence of the above supposed observation nor by the above hypothesis for the supposed observation.

Of course, specific processes could cause some cyclic process in evolution. A population overshooting carrying capacity could go under an oscillatory behaviour around this carrying capacity. As population size affects genetic diversity, such cyclical behaviour can have some impact. However, this is quite negligible. Also, there might be fluctuating selection (typically fluctuating on a seasonal basis) but this tends to be rather negligible for species of long lived individuals. I am sure you can think of some complex mechanism in structured populations would could yield to some oscillatory behaviour as well.

  One can go one step further and see the considered genetic pool in a given range as a quantum-like system governed by some kind of Schrodinger's equation. I think here of a theoretical framework like Laurent Nottale's scale relativity that could explain these similarities.

I don't understand that part. I know pretty much nothing in quantum physics (have basic understanding in general relativity but not in Nottale's attempt to merge relativity and quantum physics). You might need to expand your thoughts I guess if you want biologists to understand where you're heading. However based on the above, I suspect, there is no reason to think this cross-talk would matter in any way.

  Have such questions been considered so far?

I doubt so, because I don't think any of it makes much sense (no offense).


Confusion on polarity and hydrophobicity of Proline, Tyrosine and Cysteine? I will list here several sources that state differently on the polarity and hydrophobicity of Proline and Tyrosine:

From the article Amino Acid on Wikipedia, it states that Proline is a special case, Tyrosine is hydrophobic and Cysteine is also a special case.

From Khan academy, it also states that Proline is polar, Tyrosine is nonpolar and Cysteine is polar.

However,

From Pearson Prentice Hall's Biological Science, it states that Proline is nonpolar, Tyrosine is polar and Cystein is polar.

From BioNinja, it states that Proline is nonpolar, Tyrosine is polar and Cysteine is nonpolar.

On Wikipedia,

The article Proline supports Proline is nonpolar.

The articleTyrosine supports Tyrosine is polar and hydrophilic.

The article Cysteine states that Cysteine is polar and hydrophobic, AS WELL AS Tyrosine.

To summarize the result, I'll put them in the following table

Please help me to clear out the confusion, why the polarity and hydrophobicity of these amino acid are not agreed with each other?

TL/DR: these are borderline, complicated cases. There is no broad consensus on whether cysteine and tyrosine should be considered hydrophobic or polar. Proline is clearly nonpolar though.

The reason for the confusion is that are there several ways to define and measure polarity and hydrophobicity for amino acids. First, the polarity and hydrophobicity of the free amino acid is very different from that of the amino acid side chain in the context of a peptide (protein). I assume you are interested in the latter.

Polarity is rather difficult to define for amino acids. The dipole moment is the usual measure of polarity, but this depends on the molecule's geometry, and consequently is only well-defined for small molecules that cannot "wiggle" around, such as water. Larger amino acids side chains can wiggle quite a bit, and their dipole moment is difficult to define. Instead, polarity is usually given by rules of thumb like "hydroxy groups are polar" and "aromatic rings are nonpolar. But then there are borderline cases like tyrosine that has both an aromatic ring and a hydroxy group.

Hydrophobicity is related to polarity, but it is an experimentally measured quantity, usually determined by how an amino acid partitions between water and nonpolar solvents, or by observing how it orients in folded proteins (towards or against the water solvent). More detailed information is found here. But the results of such experiments don't always agree, and so amino acids which are borderline hydrophobic/hydrophilic can be difficult to classify. For example, for two amino acids X and Y, we might find that X dissolves better in water than Y, so X appears more hydrophilic in this sense; but at the same time, X could also partition better into a lipid bilayer, so in this sense X appears more hydrophobic than Y. In such cases, the various scales of hydrophobicity will differ.

For these reasons, there is disagreement on whether some amino acids are polar/hydrophobic. With this in mind, here's my two cents on the amino acids you mention:

Proline is a bit special in that it does not have an -NH3 group; the amine nitrogen binds to the side chain -- it is more of a "loop" than a chain -- and the peptide bond is different. But this "side loop" clearly has no polar group, and I think there is good agreement that proline should be considered nonpolar. The Khan Academy page is probably mistaken on this one. Proline is intermediate in hydrophobicity.

Tyrosine: As mentioned, polarity of the tyrosine side chain is unclear since it is quite large and has both polar and nonpolar groups. Tyrosine is somewhat hydrophobic, but among the amino acids, it places itself near the middle on most hydrophobicity scales. So tyrosine is a borderline case, which explains why different sources disagree.

Cysteine is special in the context of proteins, since cysteine residues often pair up via disulfide bonds, and this changes its properties. By itself, the -SH group is polar (although less so than an -OH group) so the cysteine side chain is somewhat polar. It is intermediate in hydrophobicity as measured by solvent partitioning. Cysteine was considered hydrophobic based on the observation that cysteine is often found in the interior of proteins, away from the water solvent; but this is largely due to its ability to form disulfide bonds.


Confusion regarding seedless grape and the normal process of germination In general, does seedless grape by definition contains seed or is the seed small enough that the process of ingestion creates the illusion that there is no seed?

If the latter is true, is the seedless grape capable of germination?

Lastly does the fruit part of the seeded grape function as an incentive for animals to ingest it and provide nutrients for seeds in the form of feces, or can it function as nutrient itself?

Thanks

The seedless grape technically has a seed, but the seed has no hard outer shell and is microscopic/invisible. These seeds aren't viable. Technically you could isolate out the seed tissue from the grape and grow it in specialized germination medium, but that process also works for any other part of the grape plant. Hooray cuttings! Certainly the seedless grape would not grow if you put it in the ground.

The fruit part of the seeded grape is 'bait' to get animals to ingest the grape and carry the seeds within inside their digestive tracts. The goal is distance, but the surrounding feces provides bonus nutrients. The fruit is not designed to feed the seedling grape, but instead to act as bait for herbivores. The grape is mostly sugars and water, which makes them excellent bait but not amazing plant food. Plants can make sugar from the sun and pull water from the ground, but nitrogen and phosphorus are harder to come by.

Contrast fruit (which are for animals) with coconuts, which are examples of large fruit storing lots of calories for the seedling itself. The coconut flesh isn't as sweet as fruit, and it's much harder to get at.


Fossils of intermediate stages? If Humans are evolve from Monkeys, there must be stages in the evolution process, when it was 1% human and 99% monkey, 2% human and 98% monkey  and so on. This is because evolution was a very slow process that occurred in a span of thousands of years. So we expect there must be fossils of this intermediate stages under earth. These intermediate-stage fossils must be many times in no. as compared to 100% human or 100% monkey.

But why do we do not discover these intermediate fossils?

We do, all the time. Here's a nice graphic from Dr. Douglas Theobald. (Images copyright 2000 Smithsonian Institution.):

That's 14 Hominid species, ranging from about 4 M.Y. ago to a modern human skull ("N").

Here's a nice genealogy as well (although these change frequently as more evidence is gathered):


Why do almost all SNPs have two alleles? Reading the Wikipedia page for SNPs I find the sentence "Almost all common SNPs have only two alleles." This is consistent with terminology elsewhere, such as the therm "Minor allele frequency", which references the least common allele, which implies there are generally only two alleles for a given SNP.

But there are 4 common nucleotides, A, T, C, and G. Why wouldn't it be common to have 3 or 4 alleles at a certain location? The only way this seems possible to me is if strand is ignored, and so at any given location "A" and "T" are considered the same allele and "C" and "G" are considered the same allele. Is this the case, or am I misunderstanding things.

Well, though it is possible to have SNPs of more than two alleles, and some exist, due to the low probability of having a basepair change twice in the same base-pair (there are aproximately 3.000 Mb in the human genome) and have it in more than 1% of the population (remember we are talking about single nucleotide polymorphism) to classify as a polymorphism is a very rare phenomenon.

I can check the maths for it if you need it, but it's just matter of probability.


Is an attraction to studying the philosophy of biology a good reason to pursue grad studies in the field? I have always leaned more towards questions surrounding psychology, sociology, and philosophy but fate has me graduating with a BSc in Biology this year. Would it be smart to pursue it further more for the aesthetic beauty I find in its ability to shed light on questions beyond itself than for the science purely in itself?

In my opinion, yes and bioethics is a very interesting domain.
 First, there is a growing interest in ethics (which is a branch of philosophy) in the fast-growing field of synthetic biology ("next-generation" genetic engineering, the design of new organisms, genetic manipulations in humans etc.). In many publications (check out "synthetic biology" and "ethics" on google) and conferences, people are saying how far behind is bioethics, compared to synthetic biology. There are many burning questions such as: If we create new organisms, should we release them to the environment? Should we edit the human genome? To what extent? (Just curing illness, or maybe also to improve traits?) Should this ability be democratized?
Should a person's genetic information be used when looking for a job? Insurance? And so many more questions, not to mention the bioethics of the state healthcare (compulsory vaccinations etc.)
There are a lot of scientists that know nothing about philosophy and a lot of philosophy experts that know nothing about science. There are not enough people who know both and can help with these question.


How to obtain raphides from plants? I recently found out that certain plants produce needle-shaped crystals called raphides. I am a physicist and I have an experiment in mind that could use these needles, but I would need to extract them from the plant and keep them in a liquid solution somehow.

How can I do this? Is this possible/hard to do? Does anybody know how to do this or have any experience?

Searching for raphide purification I came up with a paper where they isolate these crystals from kiwi fruit:

Konno, K., Inoue, T. A., & Nakamura, M. (2014). Synergistic defensive function of raphides and protease through the needle effect. PloS one, 9(3).

Does that help?

Note, however, that while according to this paper these large crystals can be kept in suspension that isn't the same as a solution ...


Simplest Biological Organism? What is the simplest biological organism from which a DNA sample has been or could be obtained?  Could the resulting DNA be processed and examined in such a way that the resulting information would give biologists a rudimentary understanding of life's minimal requirements?

Could not fit in a comment...

This post (and the excellent answer from Richard Smith-Unna) lists the species that have the smallest genome that we are aware of in different clades.

Yes we can/could sequence these tiny genomes and try to understand what each sequence does. I think that to understand the minimum requirements for life you will mostly be interested in theoretical cytology and synthetic biology than in sequencing simple genomes.

Note that the basic requirement really depends on how you define life. Is a virus alive although it has no metabolism? Would a self-replicating RNA be a living thing? Because we were able to artificially synthesize self-replicating RNA. While the subject is interesting, the main issue is a purely philosophical one: How do you define life?


Is forced cell growth related to apoptosis? Could an instance of forced cellular growth cause some cells to have their self-destruct mechanisms to malfunction or 'turn off'thus preventing apoptosis?

It is trivial to assume that forced growth will overcome apoptosis which is what you see in the immortalized cell lines and in cancer.

But the interesting thing is that there are instances in which forced growth causes apoptosis. The classic example is of the brain in which expression of SV40 t-antigen to make cells proliferative actually caused loss of tissue [1,2].

Knockdown of Aif (apoptosis inducing factor) also causes neurodegeneration and thymic hypoplasia by causing increase in oxidative damage.


Are Y spermatocytes faster but less resilient than X spermatocytes? I have heard somewhere (but did not find any suitable reference) that spermatocytes carrying a Y chromosome are usually faster but less resistant than those carrying an X chromosome.

Is this true? If so, which are the actual reasons?

There is a remote but theoretically plausible explanation indeed for the difference in speed, as the Y chromosome is much smaller and lighter and thus would make the Y spermatocytes less heavy than the X spermatocytes. Possibly, the larger number of genes on the X chromosome (missing in Y spermatocytes) could imply that they can still have some incremental translational activity.

I searched and found a letter which clearly mentions about misinformation that sperm with Y chromosome swims faster than X carrying sperms.I think this link may help https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1440662/

The letter says "The widely held idea that spermatozoa bearing the Y chromosome (Y sperm) swim faster than those bearing the X chromosome (X sperm) seems to have originated from Shettles's work in 1960, using phase-contrast microscopy.He claimed to have observed, “two distinct populations” of spermatozoa. After attempting to count the chromosomes, he concluded that the smaller heads contain the Y and the larger the X chromosome. There were no intermediate types.
The following year he reiterated these findings, adding that smaller headed spermatozoa can migrate more rapidly and fertilize the egg more often in the distal part of the tube.
Reading Shettles's reports in Nature and other peer-reviewed journals, many researchers thereafter believed that Y sperm swims faster than X sperm. The finding particularly influenced research on sperm separation.

Although several attempts have been made to correct this impression, it was not until the development of computer-assisted sperm analysis (CASA) that reliable observations could be made. So far, researchers have found no morphological differences between human X sperm and Y sperm.4 Neither mature sperm nor their precursors possess significant morphological differences between X and Y genotypes, and Y bull sperm does not swim faster than X sperm."

You can see the reference and read more
1. Shettles LB. Nuclear morphology of human spermatozoa. Nature 1960;186: 648-9. [PubMed]
2. Shettles LB. After office hours: conception and birth sex ratios: a review. Obstet Gynec 1961;18: 122-30.
3. Moruzzi JF, Wyrobek AJ, Mayall BH, Gledhill BL. Quantification and classification of human sperm morphology by computer-assisted image analysis. Fertil Steril 1988; 50: 142-52. [PubMed]
4. Hossain AM, Barik S, Kulkarni PM. Lack of significant morphological differences between human X and Y spermatozoa and their precursor cells (spermatids) exposed to different prehybridization treatments. J Androl 2001; 22: 119-23. [PubMed]
5. Penfold LM, Holt C, Holt WV, Welch DG, Cran DG, Johnson LA. Comparative motility of X and Y chromosome-bearing bovine sperm separated on the basis of DNA content by flow sorting. Mol Reprod Dev 1998;50: 323-7. [PubMed]

Hope this help!


How Would I Isolate and Amplify a Viral Enzyme? what procedures would I use to isolate and amplify integrase? If I am trying to study the integrase enzyme which is found in HIV how would I
1) destroy the viral capsule to release its contents.
2) separate Integrase from other enzymes and the viral DNA.
3) make copies of the enzyme for testing.
Any help would be greatly appreciated!!

Each virus would contain extremely low amounts of enzyme (probably a few individual molecules, at best); collecting and concentrating enough viruses to extract a significant amount of enzyme would be long and difficult, if at all possible.

The usual strategy in research laboratories is to clone the nucleic acid sequence coding for this protein (either by direct amplification from an HIV-infected cell, or by synthesizing a piece of DNA in vitro) and integrate it in an expression vector, that is, a larger piece of DNA, usually circular, suitable for integration in a host cell (human, or even bacterial) and carrying the sequences necessary for persistence and gene expression. This way you can produce thousands of copies of the enzyme you are interested in in each cell, and you can then purify a significant amount of integrase to study it.

To make purification easier, it is common practice to add to the gene a sequence coding for a "purification tag", that is, a few extra amino acids that have special properties that make the final protein easier to purify. Stretches of 6-8 histidine residues are very commonly used. The assumption is that the protein carrying this tag will have an activity similar to the natural enzyme, after purification.


What is the relationship between radiation and evolution? There is always a certain amount of background radiation present, for example due to ionizing radiation from the sun and other stars. Also certain materials like granite may emit relatively large amounts of radiation.

Ionizing radiation may cause mutations in the DNA (Gevertz et al, PNAS 1985). Mutations, in turn, may lead to altered phenotypes. Altered phenotypes and survival of the fittest are key to evolution and formation of new species.

What is the (relative) contribution of background radiation on the formation of new species?. In other words, is background radiation a critical component in evolution and would the course of evolution have changed substantially when there would be no such background radiation?

Is background radiation a critical component of evolution? No, it most certainly is not.

The DNA replication and DNA repair mechanisms aren't perfect and errors happen without any external cause or catalyst. You could say mutations happen on their own. There are mutagens that also cause DNA damage or mutations, but they're merely affecting the DNA replication in a negative way, causing it to err more often.

So, the effect of background radiation isn't the key here, the key is that the biological processes of DNA replication and repair are not infallible, although radiation does increase the error rate (the rate of mutation) just like many other mutagens do.


Are there biological ratchet cycles that are small in number? I recently came across the strange factoid that all animals that can jump do so to roughly the same height (within an order of magnitude).  The argument was that the work done by muscles in a single contraction is proportional to their mass, and the amount of energy required to jump is also proportional to their mass.  The secondary issue of power could be solved by an approach like the click-beetle uses, where they store the energy in their shell slowly, then release it quickly.

I'm an engineer, so my first thought is that a ratchet could be used to circumvent this sort of limit.  If I could cycle a muscle 2-3 times and use a ratchet to store that energy, I could release 3x more energy and jump higher.  As an engineer, it seems like a no-brainer.

But I can't seem to find any biological example of such a ratchet.  The closest I could find was the muscle proteins that cause contraction in the first place.  But that didn't fit the image of the structure I cared about because it was literally millions of these ratchets and the result felt "too smooth" for the concept I was searching for.

So my question is whether biology has a structure that operates like:

Powered by a muscle that gets to contract multiple times (or another chemical process which cycles a small number of times. 2-10 is fine, 10 million is not)
Stores the energy of each contraction
Releases that energy in one burst.

Mentally I'm thinking of a ratchet that I could crank down with 3-4 pulls of a lever, and then release all that energy at once, but I'm open to other biological structures which meet the above requirements.

First I would in return ask why the actin-myosin coupling should not qualify - the many repetitions of this contractile unit never contract at exactly the same time, and their combined contractile force certainly accumulates in a ratchet-like fashion across the microsecond time scale (with other units contracting before previous units have relaxed). Just because it's a lot of them doesn't make it less ratchet-like :)

With this restriction though, and looking for a "macro-scale" example, I am not aware of anything fitting your description. If I think about it as follows, it also seems intuitive that this wouldn't evolve.

A ratchet as you describe, let's say able to store up x contractions of a muscle for instantaneous release, can also be thought of as a series of x muscle contractions coupled in series across time. It would be equivalent in output to coupling x muscle contractions across space and executing all of them simultaneously. In other words, growing x times the muscles achieves the same benefit.

When it comes to the probability of evolving, what's more likely: an entirely new mechanism to store mechanical energy across time and allow building up, or a simple duplication of the same tissue? The currently existing muscles answer this question: duplication. This can be seen in the different structures that muscles have across living species (muscles in animals, similar contractile mechanisms elsewhere).

The smallest contractile unit in muscles are myosin heads coupled to actin filaments. Duplicate this unit (repeatedly) in two dimensions of space to obtain a myofibril. Multiply the myofibril many times and you reach a single muscle fibre. In fruit fly larvae, this is where it stops - each muscle consists of a single fibre. By the time you're at the adult fly though, the muscles that power the wings consist of a handful of packed parallel fibres. As you go down other routes along the evolutionary tree towards the mammals, you end up at muscles that consist of masses of fibres packed into fascicles, of which many are packed into an individiual muscle. As described above, at each level you have a "many-ratchet", because fibres and fascicles don't contract at exactly the same time everywhere.

So yes, you could evolve a ratchet. Or you could just evolve a bigger muscle. If many animals happen to stop evolving more muscle at around the same absolute potential jump height, that to me suggests that this is a universally beneficial jump height to evolve for terrestrial animals regardless of body size.


Linkage disequilibrium with multiple alleles and loci Linkage disequilibrium $\left(D\right)$ for two bi-allelic loci is defined as:

$$D=X_{11}X_{22} - X_{12}X_{21}$$

where $X_{11},\ X_{12},\ X_{21},\ X_{22}$ are the frequencies of the haplotypes $A_1B_1$, $A_1B_2$, $A_2B_1$, $A_2B_2$ respectively (the subscript number correspond to the two different alleles and $A$ and $B$ correspond to the two different loci)

My questions are

How is $D$ defined for more loci and a greater number of alleles?
How is $D$ defined when the number of alleles differ from locus to locus?

LD describes the associations among alleles at different loci. For anything more than two bi-allelic loci, you need more than just one number to fully describe the associations. For instance, if we have three bi-allelic loci 1-3, we need the three pairwise LD coefficients, plus one extra three-way coefficient. In general, if we have $K$ loci, and the $k^\text{th}$ locus has $n_k$ alleles, there are $\prod_k n_k$ possible haplotypes, so to fully describe the state of the population we need $\prod_k n_k-1$ haplotype frequencies. If we instead want to use allele frequencies and associations, we'll therefore need $$\prod_k n_k-1-\sum_k(n_k-1)=\prod_k n_k-\sum_k n_k+k-1$$ LD coefficients. (Note that each locus is described by $n_k-1$ allele frequencies.) This means that things get complicated pretty quickly with many loci! If you want to dive into the details, check out Barton and Turelli (1991) and Kirkpatrick, Johnson, and Barton (2002).


How many different smells can a human recognize? How many different smells can a human recognize?

If the space of smells is not discrete, how many dimensions it has (for example, the space of colors is three-dimensional).

As nobody is suggesting an answer I'll give my guess that I already discussed in the comments and give some extra details about ongoing debates on the subject.

We'll start with the sense of color sight in order to make easier. One can argue that we see in 3 dimensions because we use three cells which level of activation inform the brain of the color. I guess that the whole 3D space delimited by the maximum level of activation of each three receptors can be used. Therefore, it is nothing else than the number of receptor that determine the number of dimensions in which we can sense. Now it is assuming that each receptor can send signal of different strength information of the intensity of the light or smell.

According to wikipedia. Mammals have about thousands of genes that code for olfactory receptors. Moreover, the question of how these receptors work is still debated

  In mammals, each olfactory receptor neuron expresses only one functional odor receptor. Odor receptor nerve cells function like a key-lock system: If the airborne molecules of a certain chemical can fit into the lock, the nerve cell will respond. There are, at present, a number of competing theories regarding the mechanism of odor coding and perception. According to the shape theory, each receptor detects a feature of the odor molecule. Weak-shape theory, known as odotope theory, suggests that different receptors detect only small pieces of molecules, and these minimal inputs are combined to form a larger olfactory perception (similar to the way visual perception is built up of smaller, information-poor sensations, combined and refined to create a detailed overall perception).[citation needed] An alternative theory, the vibration theory proposed by Luca Turin, posits that odor receptors detect the frequencies of vibrations of odor molecules in the infrared range by electron tunnelling. However, the behavioral predictions of this theory have been called into question. There is no theory yet that explains olfactory perception completely.

Note: the two competing theories for color sights: Opponent process and Trichromacy

Hope this helps!

I think this question would also be a good fit for cognitive science beta.


Why are there no Nissl bodies in the axon? What could be the significance of not having Nissl bodies (endoplasmic reticulum) in the axon hillock (a part of the cyton) and axon? Does it have something to do with the processing of action potentials?

What prevents Nissl bodies from entering the axon hillock even though they can enter dendrites (which are much narrower)?

Molecularly, Nissl bodies are the densely clustered ribosomes on the ER. The basophilia is due to the RNA in the ribosomes. The question you have raised is a very significant one. For perspective, I quote a book Fundamental Neuroscience, 2002 (2002 is pretty old for neuroscience!)

The hillock is a region where materials either are committed to the axon (cytoskeletal elements, synaptic vesicle precursors, mitochondria, etc.) or are excluded from the axon (RER and free polysomes, dendritic microtubule-associated proteins). The molecular basis for this sorting is not understood. Cytoplasm in the axon hillock does not appear to contain a physical "sizing" barrier (like a filter) because large organelles such as mitochondria readily enter the axon, whereas only a small number of essentially excluded structures such as polysomes are occasionally seen only in the initial segment of the axon and not in the axon proper.

But a recent paper GG Farias et al. 2015, proposed the presence of a special area in the axon hillock known as the Pre Axonal Exclusion Zone (PAEZ) that tries to explain this polarized sorting by differential binding of microtubule motors.

Although the paper mainly talks of the sorting of axonal and somatodendritic vesicles as seen in the picture, they also seem to apply for the RER which actually are the basis for Nissl's granules.

This structure excludes not only somatodendritic vesicles but also larger organelles, such as the Golgi complex and the rough ER, in effect constituting the cytoplasmic boundary for the somatodendritic and axonal domains..... The exclusion of the rough ER and Golgi complex, in addition to somatodendritic vesicles, at the PAEZ suggests that a common restriction mechanism may operate for all of these organelles.

Well, as you might have understood by now, it's not a matter of the size of the axon/ dendrite since same sized vesicles are being diverted in either direction and as previously mentioned, even mitochondria enter the axon.


Glycocylation or glycosylation? I came across a few sources that refer to glycocylation. Is this the same as glycosylation?

See for instance page 237, or the abstract in this paper.

"glycocylation" - 1210 search results on google
"glycosylation" - 5.98m search results on google

Yes, glycocylation is same as glycosylation. You can check out following links which explain glycocylaion same as post translational modification named glycosylation.

https://www.semanticscholar.org/author/Haudhiya/93411308

https://grantome.com/grant/NIH/R01-DA004166-05

https://quizlet.com/137217422/lecture-10-a-biochem-final-flash-cards/

https://books.google.com/books?id=3RbT3cpdCc0C&pg=PA508&lpg=PA508&dq=glycocylation&source=bl&ots=qIwbK6-ZdP&sig=ACfU3U18W_rG0D53R67_fzAywtMXGye5NA&hl=en&sa=X&ved=2ahUKEwjKrvfJp_foAhW3knIEHWLVB8gQ6AEwFnoECGQQQw#v=onepage&q=glycocylation&f=false


Why does the nerve action potential needs potassium? When looking at the action potential generation I do not understand why potassium is needed. I know that potassium is used to repolarize the cell. But why are sodium channels and/or sodium pumps not used to push the cell back into its resting potential?

For example in this video at minute 2:00, sodium is pumped in, and potassium out of the cell. But both are positive ions. You get a less negative membrane potential but wouldn't it go faster if the potassium ions stayed in the cell?

Has potassium an extra property compared to sodium that makes it especially suitable for the repolarization step?

The action potential is mediated by the opening of Na+ channels, which happens in the order of milliseconds (e.g., Aldrich & Stevens (1987)). Repolarization occurs through the opening of K+channels. Their opening is delayed by a few milliseconds (Purves et al., 2001) to allow Na+ to pour into the cell through Na+ channels. After that delay, the opening of K+ channels occurs also in the order of milliseconds. After these two processes are over, the membrane enters a refractory period, again on a millisecond scale. Then the membrane is ready for another action potential.

The Na+,K+-ATPase, on the other hand, has nothing to do in the action potential process as such. It operates much more sluggishly and it can by no means keep up with the rapid channel gating during action potentials. Instead, the Na+,K+-ATPase activity operates at the background to maintain the overall ion homeostasis. As an analogy, the power adapter of a laptop PC can never keep up with the processor speeds; instead, it functions in the background keeping the battery charged.

Then why two different ions? Because two different species of ions are necessary because they fulfill opposite roles in terms of polarization and reploarization.

References
- Aldrich & Stevens, J Neurosci (1987); 7(2): 418-31
- Purves et al., Reconstruction of the Action Potential. In: Neuroscience, 2nd ed. Sunderland (MA): Sinauer Associates (2001)


How long can E. coli stocks be stored at -20°C? I'm volunteering for a biohacker lab - biocurious in Sunnyvale.  The have a pretty good set of equipment - gel boxes, incubators, but they don't have a -80°C freezer yet.

I'd like to set up some glycerol stab stocks of some E. coli strains, but i'm told even untransformed (i.e. no plasmid) bacteria will get funny after a while at -20°C.  It would also be good to hear how long you can keep a plasmid transformed strain at -20°C.

Can anyone be specific about what happens and how long it takes when you store them at -20°C for long periods of time?

I have done a little reading for competent cells and I guess they stay active for about 4 days without a -80°C freezer.

I think that cells get damaged at -20°C not because they are stored for a long period of time, but because they undergo cycles of thawing and freezing (the ice crystals that form damage them).

I never keep cells at -20°C. I store them at -80°C in 50% glycerol. The idea behind the glycerol is that it serves as cryoprotecor. It forms hydrogen bonds with the water molecules and thus it disrupts the water-water hydrogen bonds. As a result, it disrupts the crystal formation of ice, and the cells don't freeze. The freezing temperature of glycerol is −37.8 °C (60-70% glycerol in water), which means that at -20°C glycerol does not freeze and thus it cannot protect the cells from damaging from ice crystals formation.


How cnidocytes work? I have googled  for the structure of cnidocyte but images of google is unclear or complex .so please draw a simple understandable structure of cnidocyte .I know that cnidocyte works by osmosis but I don't know how exactly osmosis make cnidocyte to function .so please explain the mechanism of cnidocyte.

A cnidocyte is a poison-loaded harpoon connected to a pressure plate, implemented at the microscale level in a cell. Something triggers the plate, the harpoon jets out. Simple enough.