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How much does sprayed water remove bacteria?
I was quite skeptical about some company claiming that their device was able to suppress 99.99 % of bacteria.  Then I read a report testing the germicidal effect of their device, from a large and independant testing laboratory.
The device was tested against a number of bacteria, including Salmonella, Escherichia coli, Staphylococcus aureus, or Listeria.
They incubated contaminated Petri dishes, then used the device, then incubated the Petri dishes again.  It appears that the test samples had a CFU level log-reduced by 4 to 6 (i.e. the number of bacteria is reduced by a factor of 10,000 to 1,000,000) in most cases when compared to control samples, which supports the claim.
However the device implies spraying water, to which the control samples have not been subjected.  I am curious about how much this simple spraying may affect the results.
Would rinsing the dishes with sprayed water significantly reduce the amount of bacteria ?

In which light does that spray? Is it sunlight ?

@JM97 There is no mention of the lighting, but I'd rather guess white fluorescent tubes or bulbs, according to pictures.  It may also be worth mentioning that the water temperature ranges from 20 to 30 °C.

@JM97 Would lighting have a significant effect ?

Uv light kills bacteria, and spraying provides more exposure.

Though conditions are not exactly the same (the water is not sprayed, the duration of water exposition is different, and samples are not Petri dishes ; I am not competent enough in biology to compare methodologies), I found two relevant papers.
Listeria innocua/monocytogenes, pure rinsing
The first paper used Listeria innocua "as a surrogate for L. monocytogenes", while the EMSL report linked in the question tested the latter.
They found the following bacterial log-reduction after rinsing for 15 s under running cold tap water at room temperature and without prior soaking :

on brocoli and lettuce : 1.41 (96.11 %) ;
on apples : 2.01 (99.02 %) ;
on tomatoes : 2.10 (99.21 %).

To be compared to the report from the EMSL which found, after spraying modified water for 10 s on an inoculated Petri dish (which surface is obviously smoother than that of a tomato) :

at 20 °C : 4.24 (99.994 %) ;
at 25 °C : 3.01 (99.903 %) ;
at 30 °C : 3.37 (99.957 %).

Note that although not mentioned, uncertainties on the EMSL numbers must be fairly large since the quantitative counts are below the detection level of the apparatus (but would actually make the numbers conservative…).
Link to the paper : Efficacy of Home Washing Methods in Controlling Surface
Microbial Contamination on Fresh Produce (open access PDF), Agnes Kilonzo-Nthenge, Fur-Chi Chen, Sandria Godwin, Journal of Food Protection, 69, 2, 2006.
(NB : it contains further testing which are out of scope for this question but may be of interest, e.g. soaking, rubbing or wiping with paper towel.)
Escherichia coli O157:H7, rinsing while thoroughly rubbing
The second paper tested Escherichia coli 0157:H7, which has also been tested by the EMSL.
The paper reports the following log-reduction after thoroughly rubbing during 15 s under running tap water (no indication of temperature, but flow of 2.0 L/min ; the values in the abstract seem wrong for tomatoes, here are the in-paper values) :

lettuce leaves (not rubbed ?) : 1.16 (93.08 %) ;
cabbage leaves (not rubbed ?) : 2.02 (99.05 %) ;
lemons : 4.10 (99.99 %) ;
tomatoes : 5.78 (99.9998 %).

Note that the same reduction is reached for tomatoes after only 8 s of washing.
To be compared to the EMSL results (sprayed "modified" water, 10 s rinsing, no rubbing, Petri dish) :

at 20 °C : 5.67 (99.9998 %) ;
at 25 °C : 5.14 (99.9993 %) ;
at 30 °C : 4.88 (99.998 %).

(Same comment about uncertainties applies.)
Interestingly, in this study they also tested the effects of alkaline electrolyzed water, which may not be too far from "ionized water" (I have yet to dig into details), which itself may not be too far from what is supposed to exit the device tested by the EMSL.  And… they found no significant difference with regard to plain tap water.  (Though they did find significant effects with acidic electrolyzed water and by applying both successively — but that's out of the scope of this question.)
Link to the paper : Reduction of Escherichia coli O157:H7 on Produce by Use of Electrolyzed Water under Simulated Food Service Operation Conditions (open access PDF), Pangloli et al, Journal of Food Protection, 72, 9, 2009.


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Will daily sweeped ants eventually learn their path is a dead-end?
An ant colony (likely Lasius niger) made its way through one of our rooms, literally.  That is, they enter by a door and leave by the other, and vice versa.  Some carry eggs, but in both ways, so I'm not sure whether the nest is on one side or the other.
I sweep them outdoor everyday, but each night they repopulate the path.  Am I wasting my time or is there a chance sweeping makes them decide it's a dead-end ?
NB : Washing the floor didn't change anything.  I also tried to barricade with somehow large amounts of essential oil of Eucalyptus citriodora, but it didn't seem to help.  Anyway although suggestions to get them leave are welcome in comments, I'm genuinely interested in knowing if the sweeping strategy may have an effect or not.

Related : https://biology.stackexchange.com/questions/20431/can-ants-learn-things

I often trace the trail as far as I can away from my home and plant bait poison in line with their current path. I then use vinegar to scrub their path everywhere beyond the bait trap. The ants enjoy this new closer food and usually seem unable to find their way back into my home

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Is this a legitimate teratoma for a human pluripotent stem cell assay?
I can't quite make out this teratoma:
                                    [Source: FIG 3B]
I can kind of guess at ectoderm, mesoderm and endoderm structures based on generalized textbook developmental biology references but it looks like the stain was messed up. Shouldn't a hematoxylin-eosin stain be blue and red? Is this a legitimate confirmation of germ cell development from human pluripotent stem cells?

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Where do I purchase a fly with the collagen tagged?
Where can I purchase a fly with tagged collagen?  My senior undergraduate research paper is observing the collagen in larvae with normal diet compared to larvae with an experimental diet.  I need flies that have the protein tagged so I can observe the collagen under a fluorescent microscope.  Instead of using an expensive antibody (my budget is $300) to tag the protein, my advisor suggested purchasing stock flies that already have the tagged protein.

try bloomington (http://flystocks.bio.indiana.edu) if you work with Drosophila.

There are some more places other than what Bez has already mentioned.
See here.
However, tagging collagen may be a problem. Collagen undergoes a lot of post-translational modifications including hydroxylation and end clipping. It forms a unique structure (triplex) and adding tags may compromise its structural integrity. You can try Masson's trichome stain instead, which is used to stain collagen — a very cheap alternative.

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Unsure why Synechococcus moves at angle in cuvette
I'd really appreciate your help. I'm working with Synechococcus. In my experiment, I have Synechococcus in a solution of milli-Q water. I illuminated it with a focused white light through a pinhole and observed it using a CCD camera. The Synechococcus flows downward, which I think is due to gravity. But, in time, the Synechococcus flows downwards at an angle. Is this due to heat convection? If it is heat convection, it's strange that it sometimes stops flowing. The only visible motion seems to be Brownian motion.
Thank you your help!


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What do chimpz/bonobos/orangutangs/gorillas feed their babies with?
I just read this question and it made me curious about what a more original baby diet would look like. So, at what age do our closest relatives in the animal kingdom start giving their offspring more solid food, in addition to milk, and how do they prepare it?

You are expected to show some attempt to answer the question on your own. go on google scholar and type in chimp weening diet.

@John I googled but it was hard to find relevant keywords.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3581971/

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Does denaturing proteins lead to loss of epitopes?
I am doing an experiment where I have to do both Immunohistochemistry and SDS-PAGE. I am assuming that the native conformation of the protein is maintained in the IHC. But during the blot, we heat the protein (at least in our lab) at 95oC in mercaptoethanol to denature the protein by breaking the disulphide bonds thereby destroying the tertiary structure.
My question is when we are using the same antibody against the protein in the tissue (intact for IHC) and isolated (denatured for SDS-PAGE) protein, how can it bind both? So, the antibodies bind to the epitope based on the AA sequence or the 3D conformation? Wouldn't there be a lot if cross reactivity if it binds just based on sequence (since you could have the same sequence in many proteins, having the same conformation is much less likely)?

Short Answer - If the same antibody works both for IHC and SDS-PAGE it either means it is monoclonal against a surface linear epitope or a polyclonal antibody.
Long Answer -
Starting off, there are broadly two kinds of antibodies based on the type of the epitopes. The epitope can either be linear or conformational. Here's a couple of pictures that should clarify.

Now coming to the techniques, in IHC although there is little denaturation, one can expect the conformation to be intact. On the other hand, SDS-PAGE requires the protein to be drawn into linear structures so that they can pass through the gel.
When the manufacturer says that the antibody is monoclonal and can be used both for IHC and the blot (manufacturers do mention the compatibility of the antibody with different techniques and species), it is most probably derived against a linear peptide on the surface of the protein. This means that it would work for IHC (since it needs a surface epitope) or SDS-PAGE (which needs a linear one). May you keep in mind that, a surface epitope can either be conformational or linear. Monoclonal Abs are produced by the hybridoma technique.
On the other hand, if the antibody is polyclonal, it is much more likely that this set contains some IgGs that bind linear epitopes and some that bind surface epitopes. Thus a polyclonal antibody is much more likely to work on both SDS PAGE and IHC. It is also somewhat easier to produce, since it is essentially only purified antisera from an animal that was immunized with the antigen of interest.

Many but not all B cell epitopes will be destroyed by denaturing.  Those that are conformational will be destroyed, but there are also many B cell epitopes that are linear, based on amino acid sequence only without strong conformation dependence.
Also, depending on your IHC protocol, there's often a fixation step that involves a certain amount of denaturation, though rarely as drastic as in immunoblotting.  Conversely, some proteins are capable of at least some restoration of native conformation after they bind to your blotting substrate.
Bottom line, it's unpredictable, but it works often enough to make it worth trying.

Thanks! So, does it mean that when the Ab manufacturer says it would work both for the blot and IHC, it is a linear epitope it is binding against?

Probably, though there are also epitopes that are not linear that can make it through denaturation (I've heard; I don't know what happens with those), and as I say IHC often leads to some denaturation and blotting substrates can partially restore conformation.  Another possibility, of course, is that the manufacturer is mistaken.


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What are the differences between how glucagon and cortisol work to increase blood sugar?
As I understand it, both cortisol and glucagon cause an increase in blood sugar concentrations. However, I don't understand how they work differently or why they work separately. I would be very grateful if someone could explain the separate roles and functions of these two hormones and also the different effects that they have (I believe cortisol also has something to do with promoting lypogenesis in adipose tissue at the trunk of the body and lypolysis at the extremities).

Glucagon and cortisol are VERY different types of hormones, though each of them can affect glucose metabolism and effectively can increase glucose concentrations in the blood (albeit through different mechanisms).

Glucagon, pictured above, is a 31 amino acid peptide hormone (i.e. PROTEIN) that is released from the alpha-cells within the pancreatic islets. Glucagon travels through the blood and acts predominately in the liver on glucagon receptors. The glucagon peptide binds to the glucagon receptor on the OUTSIDE of the cell and transmits a signal to the INSIDE of the cell. This occurs when the glucagon binds to the receptor, changing its conformation or "shape" on the inside of the cell, which then causes binding and activation of a G-protein inside the cell ($G_S$). This $G_S$ protein activates an enzyme within the cell (adenylyl cyclase) to increase the concentration of a substance called cyclic AMP (aka cAMP) that activates a number of enzymes that ultimately increase the amount of glucose released by the liver. These effects are IMMEDIATE effects, which is why we sometimes give glucagon injections to treat patients with hypoglycemia (i.e. dangerously low blood sugar concentration). However, sustained glucagon signaling likely has effects on the expression of the enzymes that cause the glucose to be released from the liver as well (though that is a discussion for another question).

Cortisol, pictured above, is a steroid hormone (i.e. LIPID) that is released from the adrenal glands, specifically the zona fasciulata, which is the middle of the three 'layers' of the adrenal gland. Cortisol is referred to as a glucocorticoid and exerts its major effects through changing gene transcription in a variety of cell types. The way that cortisol does this is by binding its cortisol receptor, which is generally thought to be in the cytoplasm inside the cell. Upon binding of cortisol to the cortisol receptor, that complex is then transported into the nucleus of the cell where it binds DNA and can increase or decrease the transcription or expression of target genes. In the case of cortisol, these genes are for the enzymes that increase glucose production of the liver, and thus increase the body's capacity to maintain or elevate blood glucose. There is also some evidence that cortisol has additional effects independent of gene transcription, but that is outside the scope of this question. Regardless, the effects of cortisol on glucose metabolism are not immediate, but rather they take >30 minutes to several hours to begin to take effect.
As mentioned in the question, both glucagon and cortisol affect glucose metabolism. Cortisol also affects the transcription of a number of genes involved in adipose tissue and lipid metabolism, as well as genes that are involved in protein metabolism and inflammation. Cortisol can be injected into a patient with an autoimmune "flare-up" in order to quell the inflammation, but those are different mechanisms of cortisol than its effects on glucose metabolism. A description of those effects is also outside the scope of this question, but could easily be read about in recent reviews on cortisol available on PubMed, e.g. Recent Cortisol and Fatty Liver Review.

Good job on the molecular mechanisms. Is it really established though that the effect of cortisol on immune cell activity is distinct from its effect on glucose uptake and metabolism? Since activated immune cells are generally glycolytic, I thought the immunosuppressive effect of cortisol could be mediated by suppressing immune cell glucose uptake.

Thanks @Roland - the non-metabolic actions of glucocortioids isn't my area of expertise...but it appears that many other pathways (e.g. NF-kB and others) have been established that lead to the anti-inflammatory actions of cortisol and other glucocorticoids. See http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047790/  and  http://www.clinsci.org/content/94/6/557

Glucagon increase the blood sugar level in normal physiological pathway. It just mediate the blood sugar level when the level is too low.
On the other hand, cortisol is used when body under stress. It is used for "fight or flight" response in body, and it increases the energy production temporarily. When body is faced with stressor, the cortisol is secreted by a complex hormonal cascade, and the cortisol helps body to produce energy immediately to muscle and narrows the arteries to increase the heart rate, which force blood to pump harder and faster, and it also inhibits the activity of insulin. When body solves the problem, the hormone level return to normal.
Cortisol also can reduce the inflammation in the body, which can suppress the immune system.
Here is the paper maybe you will be interested.
Cortisol — Its Role in Stress, Inflammation, and Indications for Diet Therapy

Good article, please allow me to comment:
Both hormones cortisol and glucagon are insulin-antagonistic (=anti-insulin hormones).
Glucagon differs from cortisol because it is a peptide hormone and cannot cross cell membrane. It must be injected like insulin. Glucagon is released from α-Langerhans cells in the pancreas during the acute stage of hypoglycemia and counters insulin directly by reversing/suppressing glycogen synthesis and converting it to glycogeno-lysis (=release of glucose from glycogen). Glucagon may be used by type 1 diabetics to treat insulin shock/coma (severe hypoglycemia caused by excess insulin). Cortisol is steroid hormone. It crosses cell membrane abd binds to its nuclear receptor. Cortisol is more complex than glucagon:
1 - Cortisol regulates other glucose-regulatory hormones including glucagon and epinephrine synthesis.
The synthesis of epinephrine (adrenaline) from nor-epinephrine requires cortisol in the last step which SAME is involved.
2 - Cortisol is also involved in gluconeogenesis, the synthesis of glucose from muscle protein and other non-carbohydrates in order to sustain the brain during fasting and starvation
3 - Cortisol antagonizes insulin.
Evidence exist that excess cortisol can cause diabetes while deficiency of cortisol can lead to higher insulin sensitivity and hypoglycemic syncope as seen in Addison disease. Death may occur from adrenal crisis if Addison disease left untreated.


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What is the use of an antibody that is non-neutralizing?
When we generally speak of the immune response to viral infections, we talk of neutralising antibodies. These are antibodies that can neutralise the effect of the virus and reduce its load.
My question is, what do the rest of the antibodies produced, which are not neutralising, even do?
Is it a failure of the immune response of the body to produce antibodies that are not neutralising? But isn't binding enough for opsonisation?
How is 'neutralising' even defined? Are such antibodies neutralising just based on binding (since I assume neutralisation assays are in-vitro) or do even these antibodies require downstream antibody effector mechanisms like complement, opsonisation, ADCC etc. for neutralisation?

Which antibodies do you mean with "not neutralizing"? The ones which are generated in the process of making highly specific antibodies in the process which do not fit or the majority of antibodies which are always present in the circulation?

@Chris I dont know. I just assumed that if some antibodies are called neutralising antibodies, the others must be non-neutralising. I know, not a safe assumption, but still...

Ok , what is your knowledge about antibody maturation?

@Chris I know that the activated B-cell undergoes somatic hypermutation in the germinal centre, followed by selection of better ones by FDCs

The term "neutralizing" depends on context. In virology, it generally (not always) means it prevents the virus from binding to its receptor(s) and getting its genetic material inside the now-infected cell. Other antibodies can bind other epitopes besides the sites of binding between capsid and receptor (or enveloping membrane and receptor), yet still contribute to the immune response. Such antibodies are often opsonizing. Still more antibodies are just ineffective, a byproduct of the antibody maturation process.

Are there neutralising antibodies elsewhere? I mean, in a context other than virology?

@Polisetty sure. One example is in enzyme replacement therapy, where patients genetically lacking an enzyme in a metabolic pathway can have it replaced by injecting recombinant protein into the bloodstream. These proteins have a certain glycosylation pattern, such as high levels of terminal mannose-6-phosphate residues, and they bind the M6P receptor on target cells and are internalized. Since the injected protein is foreign to the patient's immune system, they can raise a variety of antibody responses against it. A neutralizing antibody could bind to the protein's active site, for example,

and prevent the enzyme from catalyzing its reaction. Another response, which is sometimes called neutralizing, has antibodies binding the M6P residues and preventing the protein from binding the M6P receptor. You can read about other neutralizing responses here. Typically they are discussed in the context of virology, but the diphtheria antitoxin antibody response is another good example of a non-viral response.

"Neutralizing" is not a general concept; it's context-dependent.  Most often (in virology anyway) it means that the antibodies, by themselves in a tissue culture plate, can prevent infection of the cells by the virus. Many antibodies that are "non-neutralizing" in tissue culture are probably protective in the animal, in the context of complement and phagocytic cells and so on.
That said, there's no reason why antibodies should be protective, let alone neutralizing.  Antibodies don't arise in a guided manner with foreknowledge; antibody development is driven by physical interactions between the antibody and its binding partner. If they happen to arise to something irrelevant -- an internal protein of a virus, or a pollen grain, perhaps -- then they can still be driven through priming and development and maturation and still be functionally useless, or even harmful.
On top of that, of course it would be beneficial for pathogens to be resistant to antibodies, and at least a few have evolved this ability, so for those pathogens many antibodies would be non-neutralizing and non-protective.


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Organisms with one, two, or more than two biological parents
I am interested in the generic names of organisms with one, two, or more than two biological parents. I don't know if the latter possibility is possible in nature, but if it could be, it would certainly be interesting.
Thank you for your answers.

Do you mean terms for referring to "species where reproduction mode leads individuals to have one, two or more parents"? Main cases will be roughly covered under the terms "sexual reproduction" and "asexual reproduction".

Can you please point me to a Wikipedia article with some pictures. I was wondering whether three, or more, is possible, or purely fictional. Thanks.

You might first want to read about asexual reproduction and sexual reproduction. I am not aware of a case where an individual has properly more than two parents. However, double fertilization in angiosperm might more or less be considered as such.

Very interesting Remi, I was not aware of double fertilization. Thanks for the pointer. :-)

@Remi.b I wouldn't consider double fertilization in angiosperms to be more than two parents because both sperm cells are coming from the same parent plant. Of course, self-pollinating flowering plants can undergo double fertilization as well -- in those instances, there is only one parent.


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How to cite a herbarium specimen
How do I cite a herbarium specimen that I have used to prepare a botanical description? Do I use the collector's name and number or the herbarium code and accession number? What if there is no record of the collector's name or number?

In general, the "how to cite", depends on the journal you publish. Check on their website (hot to submit) or check common journal used in your field, and copy the style used in articles.


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How did palaeontologists discover the age of the Tyrannosaurus rex named Sue?
I'm trying to understand how they discovered or speculated the age of Sue the Tyrannosaurus rex to be about 28–29 years old. How do they know exactly the age of Sue? Could it be wrong? Could it be possible that she is older then they thought — maybe 35 years old?

Dinosaur bones contain rings, similar to a tree, that can be counted to determine age. SUE was 28 when she died, making her the most geriatric Tyrannosaurus yet found. Her bones show signs of wear and even disease, including arthritis.
Paleontologists can make micron slices of bone and view the rings through polarized light, even on a microscope at 5-10x, similar to geologist mineral ID's.
https://mistralmtn.blogspot.fr/2013/03/bone-growth-rings.html

Wiki: Growth lines may be deposited in synchrony with endogenous biorhythms. For example, captive crocodilians exposed to constant temperature, diet, and photoperiod, still exhibit the periodic and cyclical skeletal growth banding of their wild counterparts.[4] Consequently, it is assumed by many paleontologists that the growth lines of dinosaurs reflect annual rhythms, and that they may be used to determine individual ages. However, in the large and long bones of many dinosaurian taxa, resorption of internal and external bone proceeds even as new cortical bone continues to be deposited, so that growth lines deposited early in development may need to be inferred.
http://tbrnewsmedia.com/wp-content/uploads/2015/05/Dinosaur-Growth-Rate-w.jpg

though could it mean sue might reach older age if yes how old im hoping 40yrs because most larger birds can reach over 30yrs

If you read about dinosaur longevity, It says that 29 is a fair old age for a T-Rex because they are related to eagles and ravens which live 20 to 30 years on average. The oldest wild bald eagle lived 38 years. 50 years in captivity. Because it has to hunt very actively, it must be in peak form every month of every year. Crocs can go 60 years but they are cold blooded. Other extinct genera than dinosaurs could manage 60-70 years perhaps.

The oldest wild tiger was 20 and the oldest bear was 39. If the T-Rex had the same health as a bird, at 32 years old, the probability that it can still catch prey with 15 tons to throw around, is slim. Spinosaurus could perhaps live to 40, because it's an agility predator too, same as an eagle, and you can imagine a 40 year old eagle fighting for territory, it would be doomed.

The oldest wild albatross is 67 years old, so perhaps a female Spinosaurus can live twice as long as a t-rex :) https://en.wikipedia.org/wiki/Wisdom_(albatross)

so trex cant live nearly 35-40yrs

so its not possible then?


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What type of bee/wasp is this?
I found some bees or wasps, in my garden.
Auckland, New Zealand
13mm long head to abdomen, fluffy on thorax and head. Abdomen is orange brown with black stripes.
The nest or hive is underground (otherwise I'd suspect honey bee, though they seem a little smaller even than honey bee workers).
I managed to catch one eventually, but then I realised the container had oxide powder, so the bee in the attached picture is a lot blacker than it was in life. It is also dead ( just in case that's not obvious)
They don't seem to be aggressive - there is a new fence being built right past their nest, they don't seem to be bothered by it.
I am a beekeeper but only beginning, so I do have honeybee workers to compare it to, but not a whole lot of experience.
NOTE: it is autumn (fall) here - high temperature was 23° c (73° f)

Wow, that stinger looks dangerous

What is the approximate size of the nest (number of individuals)? tens, hundreds? a few individuals?

As I said, the nest was underground, so I don't know how big it is. I'd say there were about 30 individuals within about a meter radius of the entrance coming or going at any time (sunny day - my beehive had about 5 times that number at the same time). I'd say thousands to maybe 10,000 inside, extrapolating from my hive, comparing apples to oranges.

It is a vespid wasp (family vespidae). Bees are generally hairy, and this one has the typical wing folding of a vespid. Genus Vespula. There is a New Zealand website that shows the differences among common NZ wasps here:
https://www.landcareresearch.co.nz/science/plants-animals-fungi/animals/invertebrates/invasive-invertebrates/wasps/identification/key-differences

All the pictures I can find of these are quite yellow - these are much more orange. Also, these pictures show a small amount of hair - these are furry like honey bees, on thorax and head

Bees are hairy on the abdomen. That is not a bee.

Rephrasing my previous comment: these are furry on thorax and head, like bees, but (unlike bees) not on the abdomen

@JayBee Vasps are often hairy on the thorax and head. Look at the link included in this answer (of google Vespula)

Looks like it might be a European tube wasp

Why do you think so? What details make you suggest this wasp rather than others?

Wasps are differentiated by their wing patterns, the way they fold their wings at rest, their eye shapes,wing veinal pattern and abdominal colouration pattern.  The sample is dead and not at rest, and is discoloured by the oxidation.  But the colouring most closely resembles the one I selected.  The rest of the characteristics are too obscured.  But there's likely a nest nearby so he could capture another one.

The head and jaws don't look like Ancistrocerus but are perfect for Vespa or Dolichovespula


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Can the sensory neuron network and the motor neuron network be considered separate networks?
I am reading up on the nervous system using Wikipedia and trying to interpret one infographic on this page:

I've always thought of the human nervous system as a singular network of neurons. This diagram however makes a distinction between 'Motor neurons' and 'Sensory neurons'.
Can the sensory neuron network and the motor neuron network be considered separate networks?
Indirectly they will definitely be interconnected (because of impulse-response relations), but physically, are they connected or disconnected?
Or are there more?
It is very well possible that I am missing some knowledge to make this question make sense.

The sensory and motor pathways can indeed be considered separately both in concept and physically. Of course the nervous systems is a single network of neurons, but that doesn't stop it from having separate components.
One can indeed often simplify neural pathways as "IN (sensory) ===> (black box with decision-making magic) ===> OUT (motor)"
Reflexes
Reflex arcs are a great way of demonstrating this separation because they do not involve the more complicated integration of the brain. Let's take the knee-bend (patellar) reflex as an example: https://en.wikipedia.org/wiki/Patellar_reflex

The diagram is correct in concept but let me add the anatomical detail to illustrate how sensory and motor pathways are separate, yet connected: When the reflex is triggered, the signal travels up from the sensory neuron ends located under the knee cap (these are dendrites) to the sensory neuron's body in the spinal chord. The sensory cell relays the signal via its axon, which then synapses with a motor neuron's body also in the spinal chord. The motor neuron then sends a motor impulse via its axon back down to the leg, where it triggers muscle contraction.
Physically, in this case there will be a separation also in nerves (at least if I may trust Wikipedia for now), where the sensory reflex neurons' dendrites travel from the leg to the spinal chord through an afferent nerve and the motor neurons' axons travel in the reverse direction through an efferent nerve. The only physical and conceptual connection between the sensory pathway and the motor pathway is the synapse between the sensory and the motor neurons in the spinal chord.
More complex sensorimotor pathways might include interneurons or integration with various circuits in the brain, but it is usually possible to define discreet separate parts of the pathway, one sensory and one motor, with the only connection being those interneurons.
Sensory and motor separation in the CNS
The central nervous system (CNS, which includes the brain and the spinal chord) is actually surprisingly organised in this regard, with quite strict separation of motor and sensory pathway components. For example, the cortex of the brain has distinct regions which contain sensory neurons for evaluation of various types of peripheral skin sensation. Separate from these are regions which contain motor neurons for movement of skeletal (voluntary-control) muscle. The interaction of these is of course more complex given that it involves skin sensation and conscious decision making in regards to movement.

Likewise, the spinal chord is structured into sensory and motor regions. In summary, the spinal chord consists of: 1) cell bodies (motor, sensory, inter; grey in the picture), 2) ascending axons (blue), 3) descending axons (red). Similar to nerves, axons going up or down the spinal chord are bundled into "tracts". Sensory axons are never bundled with motor axons, making it possible to create a map of the spinal chord in cross-section.
The tracts' names might be a bit confusing at first, but on second look are actually pretty self-explanatory. They usually contain where the axons come from and where they are going in order to synapse with other neurons. E.g. the spinocerebellar tract is formed of axons coming from the spine and going to the cerebellum. Given that the cerebellum is near the brain and the spine is further down, this is obviously an ascending tract - and ascending tracts are always sensory (because sensory information never needs to be carried downwards due to the brain being at the top).

Where it gets blurry
The sensory/motor separation isn't always as clear as I've described above. In fact, nerves (bundles of axons anywhere in the body outside of the CNS) will usually contain both sensory and motor pipelines. In particular, the cranial nerves (12 of the most important nerves) all include sensory and motor components for the respective part of the body that they manage. E.g. the facial nerve contains both the sensory connections for parts of the tongue and the motor connections that control facial muscles.
Another more complex example is pain sensation, where interneurons in the spinal chord can feed back onto sensory neurons and inhibit their signals, or axons can inhibit those packed in the same nerve bundle simply due to electrical effects.


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What are multicell spheroids?
I'm from a maths background and I'm doing some research on mathematical models of cancer. I've come across a lot of literature mentioning "multicell spheroids" in the context of avascular tumours. I know that avascular means a lack of blood vessels, but I am having trouble finding an explanation for multicell spheroids. Are these some kind of model/approximation of a certain types of tumours, or are they actually a real phenomenon in and of themselves?
It would be great if someone could fill me in on what multicell spheroids actually are!

Classical cell culture is a monolayer of cells on the surface of a cell culture dish. These cultures differ strongly from the microenvironment which cells have in tumors, as the cells only interact with their direct neighbours, but have otherwise a relatively optimal supply of nutrients and oxygen.
In a real-life tumor, a cell mass is growing uncontrolledly in all three dimensions of the space, producing these typical "knots" of tumors. As long as these are not getting supplied by own blood vessels (meaning they are vascularized) supply of oxygen, nutrients and growth factors and hormones differ very much between the cells in the outer layers of the tumor and cells in the inside. This causes different levels of stress and also physiological reactions of the cells. This looks like in the figure below (from here):

To resemble these micro-environments for research (and 2D and 3D cell culture differ quite a bit in the results), people are trying to simulate these. Technically this is achieved by embedding small amounts of cells (typically a few hundred) into a gel matrix (for example matrigel or collagen) which is getting hard, and let the cells grow in small drops. If the conditions are right, the cells will develop into these multicellular spheroids.
You can even mix different cell types (for example tumor cells and cells which are usually present in the tissue where the tumor grows) to get an even better simulation. See the references for some more details.
References:

Three-dimensional cell cultures: from molecular mechanisms to
clinical applications.
Recent advances in three-dimensional multicellular spheroid culture
for biomedical research.
Spherical cancer models in tumor biology.
Development of 3D in vitro technology for medical applications.

Very nice answer, cheers!

They are three-dimensional cell cultures according to H Ma et al. 2012.

Multicellular tumor spheroids are one of the classic 3D culture models that can be applied to the development of anticancer drugs and treatments. By mimicking the 3D network of the cellular–matrix and cell–cell interactions, tumor spheroids resemble many aspects of the pathophysiologic environment within human tumor tissue.

Classical cell cultures are usually monolayer. Many of the differences between these cultures and real-life tissues has been overcome by 3D cultures according to Carver et al. 2014.

The multicellular tumor spheroid (MCTS), a three-dimensional model that closely resembles small avascular tumors and micrometastases, has been utilized as an intermediate between monolayer culture and in vivo studies for the screening of small-molecule drugs.

So is it a 'real life' entity or is it something that is computer generated? It is real life. Let's think of an organ. It's made up of a specific tissue(s) and a stroma that contains vascular, nervous and other components that supply nutrients and limit the organ's specific tissue. This structure develops in vivo in 3D. The blood vessels will follow tissue development in a tree-like 3D structure in order to reach to all cells. But what do you do with lab cell cultures? There are no blood vessels there. How do you supply nutrients to all cells? That is why most in vitro cell cultures are developed in monolayer structure. Yet cells are 3D structures. They are joined together in a tissue by intercellular junctions. Monolayer limits this joining to a single plane. Moreover, when it comes to cancer cells which have specific properties (they lose junctions and start to move) the monolayer model becomes limited. This is how spheroids have become a better model for studying in vivo processes using in vitro cell cultures.

So is it a 'real life' entity or is it something that is computer generated? Sorry if the question is dumb but I have no experience in biology so that is all complete jargon to me unfortunately. If you could explain like I'm 5 that would be great!


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Is it possible to separate either father or mother chromosomes from a sperm?
If we were to use a flow cytometry, can it separate either the father or mother chromosomes from a sperm?

Welcome to Biology.SE. I thought I understood the question but after our discussion in the comments under my answer, I see that I actually don't understand what you mean. Can you please expand your post to clarify your question? In the meantime, I am voting to close as unclear.

There are no "mother chromosomes" in a sperm since the sperm comes from the father.  If you mean the mother of the sperm donor, there are no "mother chromosomes" because each chromosome is in general a mix of DNA from the father and the mother.

@mgkrebbs but we have 46 chromosomes from both father and mother right?So the sperm should contain 46 chromosomes can you seperate the another 23 chromosomes from the sperm?

If we were to use a flow cytometry, can it separate either the father or mother chromosomes from a sperm?

A sperm is haploid. It contains either Y or X but not XY or XX.
Sperm sorting is the process of sorting sperm cells based on specific trait of interest. Whether the sperm is carrying a X or a Y chromosome is definitely of interest to many.
There are a number of methods for sperm sorting (see wiki > sperm sorting > methods), one of which is indeed flow cytometry. Flow cytometry is typically used to separate X bearing sperms form Y bearing sperms. You should typically have a look at Beltsfield Sperm Sexing Technology (Johson et al. 1999).

I'm actually asking can we seperate those xy or xx chromosome that carry genes?

I mean the autosomes from the father or mother chromosomes

I don't understand.... Do you mean whether we can separate sperms carrying the grandmother haplotype or the grandfather haplotype? Note that segregation and recombination make that gametes carry some mixture of the two grandparents haplotypes. (Here by grandparent, I refer to the parents of the male producing the sperm). Btw, is there any reason you talk about sperms and not ovules?

I asking is it possible to empty all the chromosomes genes from the father or mother from the sperm to have either father or mother chromosomes?

The expression chromosomes genes is unclear and suggest that you don't really understand what a gene. I am still a bit unsure of what you are asking but you can't tell what chromosome come from which grandparent (whether in a sperm cell, in an ovule or in a zygote), the main reason being that recombination shuffled them up together.

if we use flow cytometry can seperate the autosomes and the sex chromosomes of the father or mother from the sperm?

I am not sure what you call mother and father. I suppose it is what I call grandfather and grandmother, right? The answer (but I am not sure I understand what you're asking) is 'no' because it makes no sense due to recombination. Even if there was no recombination, you could not because the only eventual difference between maternally inherited and paternally inherited chromosomes are epigenetic modifications (which flow cytometry won't help you to distinguish).

You are repeating the same question over and over but I still don't get it! Try to write more than a one line question. Give some context and maybe I will be able to understand what you're trying to ask. I think your question makes no sense (but might be wrong) but I can't tell what is your misunderstanding as long as you limit your phrasing to a single one liner question.

Sorry you seem confused,I will ask one more time Can sperm sorting empty either all the father or mothers genes from a sample of sperm?

I will answer one more time then :) Assuming that by mother and father you are referring to the parents of the male who produced the sperm (but you still have not explained what you actually meant by mother and father), then the answer is 'no' 1) because, obviously, flow cytometry is not able to brake and recombine chromosomes to undo what recombination just did and 2) the only potential markers of whether a chromosome comes from the 'mother' or the 'father' is a few epigenetic differences that can't be detected via flow cytometry. I'm out repeating that now! Good luck Daniel!


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Do all IgG autoantibodies lead to autoimmune diseases?
If there is a presence of autoantibody in our blood, does that mean that we are going to have an autoimmune disease? Are there some autoantibodies which don't cause tissue and organ damage?

As usual with biology, it's not that simple. There are autoantibodies present even in people without any signs of autoimmune disease. The immune system is a complex network of positive and negative regulatory cells and molecules - looking at a single component is unlikely to determine the state of the system. This is a major reason that it has been so difficult to figure out how to selectively act on the immune system to stop or prevent an autoimmune disease without compromising normal immune function.
Here's an article that expands on some of these aspects: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703183/
For example, note "Despite the physiological elimination (negative selection) or functional inactivation (anergy) of high-affinity, self-reactive T and B lymphocytes in the thymus and bone marrow, respectively, there is compelling evidence that low-affinity, potentially autoreactive cells persist and that low-affinity reactivity to self-antigens is required for survival of T and probably B lymphocytes in the peripheral immune system."
It's also important to keep in mind that affinity of Abs and receptors for antigens usually depends on additional 3rd party molecules involved in the interaction, and that a single molecule may present very differently in different situations (for example, damage or inflammation may alter some self molecules into a previously unseen configuration that stimulates self-reactivity).

Can you please add some citations to support your claims?

@MattDMo hope that helps a bit

That's a good reference for autoantibodies in general, but the original question asked specifically about IgG, which as far as I know are always associated with pathology. I suggest expanding on that, talking more about normal IgM autoantibodies and what their suspected roles may be, then talk about class switching and IgGs being essentially universally associated with disease of some sort. You have the beginnings of a good answer, though.

Yes, I interpreted the question as being very basic and not intended specifically about IgG based on the body of the question. I don't have a good feel here yet about how deep to go in a response -- thank you for your suggestions.

Thanks for your input. I understand that IgM autoantibodies undergoes class switching to IgG and becomes more specific for the target antigen. Does having IgG autoantibodies indicate that at some point in future, the person is going to develop an autoimmune disease?

@Riq generally, yes. In fact, they likely have already developed disease, as it is during that process that class-switching occurs.


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Can someone identify this Brazilian bird?
Photographing and documenting the local fauna (Brasília, DF, Brazil - Near Coordinates [-15.696506 -47.860013]), I found this rather unusual-looking bird whose name I couldn't find:

(Image was now uploaded to Wikimedia under my account "AlephGuira")
Possibly useful information:

One was seen preying on
what looked like Taturanas (https://en.wikipedia.org/wiki/Lonomia), but due to their venomous nature, I'm not sure.
The observed flock was composed of 7 birds.
There seems to be sexual dimorphism (The other one, not pictured, seems to be smaller, has shorter head feathers, whiter wings and lacks the orange-pointed beak).
They were first seen on a Pequi Tree (https://en.wikipedia.org/wiki/Caryocar_brasiliense).

These look very similar to the Guira cuckoo (Guira guira) which are found in this part of Brazil.

Source: https://en.wikipedia.org/wiki/Guira_cuckoo


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How much pressure can human withstand if inner and outer pressure is balanced?
I know human can't dive too deep because there's pressure difference between inside and outside of the body. But how much pressure can human withstand if human is breathing components that is surrounding him?
So I have two questions:
1.How much pressure can human handle if he is surrounded by regular air (also breathing air)? 2. How much pressure can human handle if he is floating in oxygen-rich liquid and breathing it at the same time (Liquid Breathing, Wikipedia)?
There's a similar question, but it doesn't have answer that fully satisfies me. Highest Pressure Human Body Can Survive In?

Welcome to Biology Stack Exchange. The physiological responses to breathing 'regular air' under pressure are very well understood (a good answer could be based on medical studies of regular SCUBA divers), whereas the liquid breathing techniques are extremely experimental and under-studied, so any answer would have to be very hypothetical. I suggest splitting these off into two separate questions, because the answers will be basically unrelated.

Most issues with typical diving technology involve compression/dissolution/ or expansion of gas. But for extreme depths, if you assume you can eliminate issues related to gases, there is virtually no limit as long as the rate of compression allows (fluid) equalization of pressure through the cell walls. Too rapid compression/expansion can result in similar affects as exposure to hypotonic/hypertonic solutions - crenation or rupturing effects. The bulk elastance of water - very 'stiff'


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Is there any research on wolf and bobcat interactions?
I'm studying interactions between North American predators, specifically wolves, coyotes and bobcats.
There's evidence from data I've collected from game cameras that suggests a significant interaction between wolves and bobcats. However, I haven't found published literature or reports on interactions between these two carnivores besides a paper by Stenlund (1955) that suggests bobcats may benefit from scavenging wolf kills.
Does anyone know of any publications in peer-reviewed literature, government reports or even reliable observations from biologists in the field on interactions between wolves and bobcats?
Thank you!

In Sweden, no clear evidence have been found for interactions between wolf and European bobcat (Lynx lynx), see Wikenros et al, 2010. There, they have studied effects of wolfs on the survival of Lynx kittens, spatial movement of Lynx and Lynx' homerange size. The study finds no significant difference in any factor with/without wolves. They also speculate that the reason for a lack of interactions is that the two species use quite different main food resources (at least in Scadinavia); Lynx being specialized on Roe deer and wolves having wider preferences, but mostly Moose.
You should also look at the report Meta-analysis  on  the  effect  of  competition  between  lynx  and wolf on their diets (Lelieveld, 2013 which might provide more information. From reading the abstract, the report indicates no effects on wolves but that Lynxs might change their foraging behavior.


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How are mitochondrial diseases like MERRF inherited?
I am doing a project on the disorder MERRF in Mitochondrial DNA. I have to make a pedigree and explain how it is transferred on from generation to generation. I know that it is inherited maternally, but I am confused about how it is inherited. Would it be inherited inherited like autosomal DNA in a Mendelian fashion? If so, would this gene be dominant or recessive? Or would the children just automatically inherit whatever gene their mothers have? Also, how would the genotypes for Mitochondrial DNA be displayed? Any other useful information on Mitochondrial DNA or MERRF would also greatly appreciated. Thanks.

You will find useful information in Wikipedia's Mitochondrial DNA article.

Thanks for the article. Does this mean that the children will have whatever gene that the mother has?

Mitochondria are primarily thought to be inherited from the mother but there is evidence now that the father can also contribute mitochondria (Schwartz and Vissing, 2002; Luo et al., 2018).
Even if the mitochondria were purely maternally inherited, a cell (including oocyte) typically contains many mitochondria and not all of the mitochondria may have the (deleterious) mutation. This phenomenon is called heteroplasmy.
MERRF is associated with a loss of function mutation in mitochondrial tRNAs (See NIH, Genetics Home Reference). The extent to which a cell will be affected would depend on number of mutated mitochondria it contains. Therefore different cells would be affected differently.
The trait inheritance would therefore not be in the typical Mendelian fashion.


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What do the text annotations in an electron micrograph mean?
I saw a photograph taken from an electron microscope, with some text.

I want to know what is the meaning of these numbers and letters?
Thank you! Regards.

The 1.40kX is the zoom (1400x), WD is the working distance (distance between the final lens and the object), 20kV is the voltage used to accelerate the electrons, 20μm is the scale.
I'm not aware of the other two.

Thank you! if the voltage increase, what will be the effect on the picture?

@French_FitGirl The voltage is used to accelerate electrons. High velocity electron beam would have a higher resolving power. However low voltage is often preferable for SEM. You can read more about electron microscopy.


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What is synaptic clearance?
Please explain what the term synaptic clearance means. For example, what would dopamine synaptic clearance be? It is important to me in context of dopamine signaling variation due to difference in synaptic clearence level.
Some gene alleles are associated with greater synaptic clearance in dopamine pathways. It used to explain dopamine level variation and throught it some brain areas activity (for example Nucleus Accumbens) difference among people with different genotypes. For more information see for example. Also, reduced synaptic clearence related to greater dopamine signaling levels. So I was interested in this term from prespective of brain activity in areas with dopamine receptors

We generally appreciate if you provide some background and show some of your own research effort. Background means some details on where you encountered this term. Background provides the context of the term  and helps in understanding its meaning (especially for not so popular terms). Research effort refers to any information that you were able to gather by searching the web or books.

Great.. Can you please add this to your question by editing it? Usually people would not go through the comments and secondly comments do not show up in searches. Finally, a question should be complete in itself.

"Synaptic clearance" is referring to the clearing of a neurotransmitter from a synaptic cleft.  A synapse is a place where one neuron can stimulate another neuron. The tiny gap between the neurons is called the synaptic cleft. The presynaptic (stimulating) neuron releases a neurotransmitter (such as dopamine) into the cleft and some of the neurotransmitter is recognized by receptors in the membrane of the postsynaptic (stimulated) neuron.  In order for the synapse to stimulate the postsynaptic neuron a second time, the concentration of the neurotransmitter in the cleft must be reduced to its original levels.  This reduction is called clearance, and can occur in several ways (mainly dependent on the type of neurotransmitter).  The neurotransmitter may be transported back into the presynaptic neuron for reuse; this is called reuptake.  The neurotransmitter may also be degraded (broken down chemically) into an inactive form.  To a lesser extent, neurotransmitter can also be absorbed by astrocytes or simply diffuse away out of the cleft.

It means what it says: clearance of neurotransmitters from the synaptic cleft. In case of DA it's mediated by DA transporters. They are there to shorten the response of DA, making the synapse ready for another signaling cycle. It also regenerates DA in case the transporters are located in the presynaptic neuron.
Reference
Ciliax, J Neurosci (1995); 75(3): 1714-23


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qPCR: do both primers have to contain a GC-clamp in order to be effective?
I'm developing software which, among other things, designs primers pairs (forward and reverse) for qPCR. In my research on various properties, I read about GC-clamps and I understand the basics of it I think. There is still something unclear to me.
Do both primers in a pair need to have a GC-clamp in order for it to be effective? Or does one GC-clamp in, let's say the forward primer, just increases specificity, and both primers containing a clam increasing it even more?

The new question is too Health'y for me to answer. Very nice edits for Health though. Likely others can answer it.

If we are adding gc clamp in both primers, the sequence should be different or same?

You can have GC-clamps (3' terminal G/C) in both primers; this may overall improve the PCR efficiency. However you should take care not to put too many G/Cs. This may lead to stabilization of primer pairs, leading to formation of primer-dimers. Also see this post: When designing primers how important is the GC clamp?
GC-clamps are not always essential and you should look at other parameters too.

So, in summary: A clamp in one primer is good for efficiency and clamps in both are better (with the right amount of G/C ofcourse). So I don't need a GC-clamp in both of them. Is this right?

@TomKral Not strictly necessary but good if you have it in both.


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How to supply oxygen to a culture vessel?
I'm reading this paper:
https://www.jstage.jst.go.jp/article/jpsa/51/3/51_0130043/_pdf
From day 17 of the culture period until hatching, pure oxygen was supplied at a flow rate of approximately 500 ml/h through the previously installed plastic tube.
What kind of hardware is used to achieve this ? I would like to test this method, but I don't have access to laboratory equipment ( meaning .. I'm not going to buy expensive equipment for this hobby project..)
I'm used to incubate eggs inside an incubator, and day 17 is approximately the day when they start chirping, and sometimes hatching, so it's my understanding that at this point the chick starts to use its lungs, and breaks the shell in search of oxygen.
Also I don't understand the airflow in this setup: when I supply 500 ml/h of oxygen, where does the displaced gas go ?

Gases are supplied to culture vessels by design. Flasks, for example, may have filtered caps that allow gas in, or microplates with lids that have enough room under the lid to allow a gas exchange interface with the culture medium. Of course with these traditional culture vessels you need to make careful consideration about fill volume, since the gases won't penetrate 100% through the culture medium.
In the case of your paper they cut a large hole in the side of the cup and plugged it with cotton, then fed a small plastic tube through into the cup. They attach a gas line and feed oxygen through the tube. The cotton plug is where the gas will escape back out without letting contaminants in, as the cotton plug acts as a filter. The system seems to have no other outlet, so it makes sense.
In order to control a gas flow rate, you need a regulator of some sort to act as an output control.


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Can a person really die quickly from biting their tongue?
A common trope in certain circles (like Eastern martial fiction), is someone committing quick suicide by biting his or her tongue.  But is this really possible?
The internet turns up millions of pages of speculation, but no Straight Dope.  People have been removing the tongues from mammals, and each other, throughout human history.  There has to be some scientific data on this somewhere.
Will an untreated, severe, lingual laceration, really result in bleed-out of an otherwise healthy human?
Or will lingual trauma facilitate swallowing the tongue sufficiently to cause asphyxiation?
What does the science say?
Thanks!

generally untreated and severe laceration of any body part can is at risk of causing death. But according to this book the tongue tends to stop bleeding quickly  (http://books.google.co.uk/books?id=a7CqcE1ZrFkC&pg=RA1-PA1014&lpg=RA1-PA1014&dq=lingual+laceration&source=bl&ots=lgjuQlh93C&sig=th6-PfF54HbnpzkFyHotBqF1Z1U&hl=en&sa=X&ei=EUYjUcmECYXVtAb9w4DYCg&ved=0CEAQ6AEwAg#v=onepage&q=lingual%20laceration&f=false)

@rg255: Excellent. This article says that Lingual artery hemorrhage is "life-threatening".  Although it's reporting an injury caused by a botched biopsy.  It's not at all clear (to me) that a sufficiently similar wound could be caused by a person's own teeth.

I guess there is an element of "luck" if suicide is the intended outcome - it will likely depend on how hard one bites, how sharp the teeth are, and how many blood vessels one punctures severely (do not try this at home)

@rg255, If it depends on hitting the artery with your teeth, it might not be anatomically possible. Hoping for some experts or citations to chime in.

Looking at the diagrams of tongue blood vessels it looks like the ranine artery runs a long way along the tongue, and if you hit enough other veins and arteries there's no reason to not expect a high enough bleeding rate

The following letter and references therein may perhaps shed some light on the matter: http://pmj.bmj.com/content/77/913/743.1.full

Thanks @jarlemag.  The references seem to pertain to five-ish cases of tongues that were amputated to some degree.  Best I can tell -- this side of the pay-walls -- is that no immediate fatalities occurred in those cases.

One of the comments expressed surprise that the patient didn't die, though, so it seems possible. I'd read the articles and post an answer, if not for the paywall!

How about biting it off and choking on it?

No, unless you like bite your hole tongue off that's not really a thing it would be like saying (with no hate of thinking your stupid), you got a cut on your leg when your messing around out side and died. and i bite my tongue allot when i am eating.

I know of an ER doctor who had a patient who removed (by biting and pulling) every last part of her tongue, she survived that (although, her ability to speak was probably shot). The stump of her tongue clotted before she could even go into shock (at least where it was really serious).
Here is a quote from the book Angels in the ER  (this is a paramedic speaking with the doc):

"Every bit of it. Gone. And the funny thing, Doc, is it didn't even
  bleed very much."
  The doctor then asked his patient to open her
  mouth... "it was gone!"

It would certainly be possible to commit suicide doing this if one was a hemophiliac or continued to remove the clot from the hole(s) in their tongue (although the latter could be a potentially painful and I have a feeling that it would take a very, very long time!).

@BrockAdams I will get you a direct quote ASAP, right now I'm not at my house and don't have the book at my disposal. There are plenty of places you can get a PDF download, and it would be chapter 11. However, if you are willing to wait a day or two I can probably get you a quote.

@BrockAdams I edited my answer.

Thanks!  Looks like a reputable counter-example.  This answer will do unless an authoritative analysis or statistical result is posted. (Previous comments are now obsolete.)


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Identifying a thin, black, worm-like creature with a hammer-shaped head
I came across the creature shown in the photo below yesterday evening while walking the dogs. At first, I thought it was an earthworm, but a flashlight revealed it to be something I had never seen before.

It is approximately 12 inches (300 mm) in length and about 1/3 of an inch (10 mm) in diameter at its maximum. It is pitch black and very shiny—like piano black. It moves very slowly, using a snake-like motion. It had a very strange head, like a hammerhead shark.
I live in Durban, South Africa, if that helps to narrow down the possibilities.
Can anyone help in identifying this creature?

Sorry, the picture is of concrete paving and yes it was moving, but very slowly, not as slow as a slug, more like a very lazy snake movement

Hi Always confused, Your suggestions are most welcome, it is the first time I am using this forum and if I came across to strongly, please excuse me, it was not intended. Using your suggestions as to what it could be, I googled "hammerhead worm" and there is an identical picture and it is called a hammerhead slug. Very interesting animal / creature. Regards,..Graham

Careful, they might be deadly :) . https://www.youtube.com/watch?v=XW8F1boWgv0

@GrahamMattsson "about 3 inches (10 mm) ". heh?? :)

@bic:  I would guess that is 0.3 inches, 10 mm, from the photo and the quoted length.

Hmm, I don't believe I have ever seen that before, but it looks  like a Hammerhead Worm (Bipalium kewense).

Fascinating. Once of your links documents this creature as being an invasive species in Texas, although I have never come across it. It's particularly interesting that it produces tetrodotoxin, probably as an aid to killing its earthworm prey.

Fascinating indeed. Here is a very interesting read about Platydemus manokwari, an invasive flatworm from new Guinea.

Sorry I meant to say that on your link to Bipalium kewense, the hammerhead worm looks very similar to the one I saw in my garden crossing the paving, but was totally shiny black and round in girth, I meant to say 3/8" and not 3 inches in diameter (10mm).

I am not sure if I should destroy it the next time I see it or should I seek advice locally, maybe capture it in a bottle.

I think this still fits your description. It can't be shown in the linked pictures, but it is shiny black

If this completely answers your question consider accepting it. It  marks the question as resolved. @GrahamMattsson

"Slug" feels like a misleading term, since that is normally a common name for some molluscs (snails), while this is  Platyhelminth (flatworm)

@fileunderwater You are right, my bad...

Thank you for your interesting comments, another misleading term is flatworm as it is actually round.

That looks like a predatory land flatworm.  They eat snails and worms.  I think they are native to New Zealand, but have been introduced to many parts of the US through ornamental plants.
https://en.wikipedia.org/wiki/Geoplanidae

The OP pretty clearly states the photograph was taken in Durban, South Africa. Additionally, none of the images in your Wikipedia link are similar to the one provided.

Missed the location.  I see that now.  In the Wikipedia article if you scroll down and look at the "variety" picture there is one that is pretty close except for it has a stripe down the back.  Incidentally, I've seen black ones that look exactly like the one pictured in OP's original question several times in Southern California.  I used to see the striped one like in the wikipedia picture frequently in Central Texas.

Hi Cowan, There is a similar picture on the subject of Hammerhead worm shown in Google images. I was very fascinated as I have never seen this before.


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Why do insects (flies) put their legs together when they die (as if they're praying)?
Other animals don't seem to have an organized pose to die in. Or do they?

A good working theory is that this is caused by Rigor Mortis and the anatomy of insect legs.
In most cases, the muscles that pull the leg down (or closer together) are larger than the ones that pull the leg up.  This is because those muscles (flexors) must support the insect's weight:
(Click for larger view)

When the muscles contract after death, the larger muscles win out, causing the legs to move together.
From Why Do Insects Cross Their Legs When They Die?:

I suspect this is rigor mortis -- that post-death stiffening that occurs due to a chemical transformation of muscle tissue -- contracting legs as much as possible in the directions of least resistance, says Brian Farrell, an entomologist at Harvard University.


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How closely correlated is the level of an snRNA with the level of its corresponding snRNP?
Let's say I am growing cells under two conditions, and let's say I measure U1 snRNA levels in both using digital PCR.  If the U1 snRNA level is reduced in one sample, how safe is it to say that U1 snRNP is also reduced in that sample?


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What would be the conduction speed of A-alpha fibers, were they unmyelinated?
It's known (Hursh 1939) that myelinated axons exhibit the behavior $v = 6d$, where $v$ is the propagation speed [m/s] and $d$ is the axon diameter [μm].
A related relation for unmyelinated axons is (Malmivuo & Plonsey, eq. 2.1):
$$v = \sqrt{\frac{i_\text{Na max}}{r_i c_m^2 V_\mathrm{th}}}$$
I want to approximate the propagation speed that A-alpha nerve fibers would exhibit, if they were unmyelinated. How could I find values for the constants in the above equation? Is there an easier way to conduct these calculations, or has there already been a study done on this?
For the (myelinated) A-alpha fibers, d = 13-20 μm and v = 80-120 m/s according to Wikipedia.

The provided relation for unmyelinated axons only holds up to certain diameter value of the axon and is valid only as long as the sodium conductance iNa is uniformly distributed along the cross-section of the axon. This explains why non-myelinated fibers are so thin, being only 0.2-1.5 μm in diameter.
In axons having a larger diameter the axon potential can only move between Ranvier nodes. If this fiber gets unmyelinated the axon potential just stops propagating, due to several reasons:

Sodium concentration through the complete axon surface is too high so that it diffuses internally along the axon and reduces the concentration gradient in the direction of AP propagation.
AP is propagated not only along the length of axon but also laterally, that leads to its flatenning over the axon surface, decreasing its amplitude etc.

Unfortunately I couldn't find the reprint of the original publication in Biofizika referenced by the webpage you provide the link to, so I cannot investigate the constraints of their model for AP propagation.
In order to estimate the propagation velocity in unmyelinated axons of large diameter I would take some theoretical papers investigating the properties of nerve fibers undergoing demyelination. Z. J. Koles and M. Rasminsky "A computer simulation of conduction in demyelinated nerve fibres", J Physiol. 1972 December; 227(2): 351–364. seems to be one of the earliest publications on this topic and it is freely available online.
In this paper the authors tried to simulate the conductance of demyelinated motor axon with diameter of 10μm and 5μm myelin sheath. They gradually decreases the amount of myelin width until 2.7% of the initial value where they saw the abolishment of AP propagation. The propagation time was 12.5 times higher than in normally myelinated fibers (for the distance where AP could travel). If we consider the initial propagation velocity being 80-120 m/s then after demyelination it is reduced down to 6-10 m/s and fade after a short travel.

Is mkm being used as Micrometre (μm)?

Yes, thank you for your comment: I used it to copy the μ-symbol and substituted it in my answer! ;-)


text:
Multistability in the lactose ultization network
Reading the paper here, I'm confused about the production of figure 4d. The method of production is detailed in the supplementary information under the heading "Theoretical phase diagram".
Specifically, I'm confused about the use of theta and what it means. I have tried reproducing the figure using MATLAB and the parameters in the paper to see whether I can understand it better, but nothing quite works out.
To be clear, the paper obtains a steady state result for a series of ODEs:
$$
    y = \frac{\alpha  (1+(βy)^2)}{ρ+(βy)^2}
$$
Then rearranges as a cubic:
$$
    y^3 −αy^2 + \frac{ρ}{ β^2} y − \frac{α }{ β^2 } = 0
$$
Apparently, a general cubic with two identical roots has the
form:
$$
    (y-a)(y-a)(y-aθ) = y^3 - (2 + θ)ay^2 + (1+2θ)a^2 y - θa^3
$$
The paper then equates coefficients:
\begin{align}
    ρ &= (1 + 2θ)(1 + 2/θ)\\
    aβ &= \frac{(2 + θ)^{3/2}}{θ^{1/2}}\tag{did you mean?}
\end{align}
And claims that these are the parametric equations that describe the graph in question. When plotting these equations, I get nothing like the graph. I can't really see where it comes from.
The graph in question and some equations are reproduced here on the last page:
http:// web.mit.edu/biophysics/sbio/PDFs/L7_notes.pdf

I don't have access to nature so I have no idea what the figure looks like. You need to post the figure.

The equation in the OP has been updated to $(y-a)^2(y-a\theta)$ which yields the correct expansion. Therefore, by equating the coefficients, we obtain
\begin{align}
\alpha &= (2+\theta)a\tag{1}\\
\rho/\beta^2 &= a^2(1+2\theta)\tag{2}\\
\alpha/\beta^2 &= a^3\theta\tag{3}
\end{align}
Using equations (1) to (3), we get the desired $\rho$ and $\alpha\beta$. Now the authors plotted $\frac{\alpha\beta}{\rho}$ and $\frac{1}{\rho}$.
By plotting $\frac{\alpha\beta}{\rho}$ and $\frac{1}{\rho}$, we can re-create the plot in Mathematica with
ParametricPlot[{1/((1 + 2 x) (1 + 2/x)), (2 + x)^(3/2)/(
  Sqrt[x] (1 + 2 x) (1 + 2/x))}, {x, 0.01, 50 \[Pi]},
 PlotRange -> {{0, .15}, {0, 0.6}}, AspectRatio -> 3/4]

If you dont have Mathematica, here is some Python code that will plot it as well.
import numpy as np
import matplotlib.pyplot as plt

fig = plt.figure()
t = np.linspace(0.01, 25*np.pi, 5000)
x = 1/((1+2*t)*(1+2/t))
y = (2+t)**1.5/(np.sqrt(t)*(1+2*t)*(1+2/t))
plt.plot(x,y)

plt.show()

Here is the Python plot which has smoother lines compared to Mathematica's plot.

Thanks! I thought something was up... Assuming their maths had been correct and the equations for rho and alpha-beta were correct, how would you go about using them? I'm a little confused about the theta?

The plot on the last page of http://web.mit.edu/biophysics/sbio/PDFs/L7_notes.pdf

Sorry could you please add a link to the wolfram alpha graph?

@user2290362 I plotted it in Python since Wolfram will only plot it if you have the full version of Mathematica.


text:
Who is organizing the heartbeat and its roles in the body?
Throughout the decades we heard that the heart is the only muscle whose nervous system is not acting. So who is he responsible for organising the heartbeat and its roles?

The Sinoatrial Node is a ganglion (clump of nerves) attached to the heart, which regulates heartbeat independently from the brain (http://en.wikipedia.org/wiki/Sinoatrial_node).
Heart rate can also be influenced by hormonal responses produced by the autonomic nervous system. To quote Wikipedia:

While heart rhythm is regulated entirely by the sinoatrial node under
  normal conditions, heart rate is regulated by sympathetic and
  parasympathetic input to the sinoatrial node. The accelerans nerve
  provides sympathetic input to the heart by releasing norepinephrine
  onto the cells of the sinoatrial node, and the vagus nerve provides
  parasympathetic input to the heart by releasing acetylcholine onto
  sinoatrial node cells.

Source: en.wikipedia.org/wiki/Heart_rate#Physiology

THANK YOU for the answer ! But what about autonomic bervous system ?

Ah yes, of course, there's that too. I updated my answer.


text:
What is the difference between polar and charged amino acids?
Chemically polar amino acids have an uneven (AKA  polar) distribution of electrons over their surface.
Charged amino acids have a charged ion in their structure. This is probably where my knowledge is a little shaky!
I guess I am confused at this point. Does this just mean that charged amino acids are really polar amino acids? If that is correct that would explain why I have seen histidine categorised as a charged amino acid, but has no clear ions.

You can see this post on why histidine has a low tendency to form ion compared to other positively charged amino acids.

A related question: http://biology.stackexchange.com/questions/23763/is-there-a-difference-between-polarity-and-hydrophobicity/23777

All amino acids with side chains that are charged at physiological pH are, by definition, also amino acids with polar side chains (e.g., lysine or glutamic acid). The converse is not true; in other words not all amino acids with polar side chains are necessarily amino acids with side chains that are charged at physiological pH (e.g., threonine or asparagine). The pKa of the nitrogen in histidine's imidazole ring is quite close to physiological pH, and in some situations would be charged and in other environments would be uncharged. In either case it would be considered polar (or largely hydrophilic in nature).


text:
What is the difference between a spore and a cyst?
Last year I read a course in biology. During that course I learnt that Protozoa like Lamblia intestinalis or Entamoeba hystolitica form cysts in unfavourable conditions.
This year I read a course in microbiology. I learnt that bacteria like Clostridium perfringens or Bacillus anthracis form spores in unfavourable conditions. So far so good. But then I learnt that prokaryotic Borrelia burgdorferi can form a cyst, not a spore.
Firstly, I would highly appreciate any comments that would cast some light on these terms.
Secondly, I would also like to know if the spore inside, say, B.anthracis is the same organism as B.anthracis that produced the spore. Does a spore and the bacteria that produced it have the same DNA sequence? In other words, if I were a sporeforming bacteria, would my spore be myself, my bodypart or my child?

I'd like to draw your attention (if you haven't already seen it) to the comments by Souvik - I've edited my answer a bit, but hopefully someone more knowledgeable will come in.

The bacterial spores you are referring to are called endospores. The spore is formed during unfavorable conditions, by duplication of the bacterial chromosomes, and consequent envelopment by various membranes and protective coatings (while still within the original cell). The spore is dormant and remains so as the outer cell degrades during harsh conditions, releasing the spore. I guess I'd call the spore a clone of the original?
You may enjoy reading the relevant sections in this book, which go into greater detail.
edit: as Souvik has pointed out, this is only one type of "protective" spore. Actinomycetes also form spores, via differentiation of the cells, and cyanobacteria form akinetes also via differentiation (but this structure is not as durable as endospores).
Information about cyst formation is difficult to find, but in bacteria it appears to develop via changes in cell wall composition.

@ddr3 why are you referring to only a specific sub-group of bacterial spores??....I am a li'l rusty on this section...but as far as I know akinetes & actinomycetes also form spores...which are not endospores....

@souvikbhattacharya ah, I missed that on the page. I think I've conflated two different things - I'll try to edit my answer but I'm not an expert on this topic. Please feel free to edit it as well.

dd3 summed up the 1st part of your q nicely.....now 'bout the second part...bacterial spore-s (not necessarily endospores only...but akinets & spores produced by actinomycets) are produced by simple mitosis...so the genetic make-up stays the same as the parent cell.....so if  you were a spore-forming bacteria, the spore would be essentially you..in scientific jargon...your "clone"...

Well, certain bacteria form endospores to tide over unfavourable circumstances. The bacterial cell withdraws its contents so as to form a spherical-shaped mass. This spherical mass is still covered by the original cell wall of the bacterium. This microscopic rounded  body  covered by the cell wall is called a endospore(endo : inside).It is just like a tortoise tucking its body into its shell. Some other bacteria , to overcome unfavourable conditions develop a hard, protective covering called cyst around themselves. When the conditions become favourable, the cyst ruptures and the bacterium emerges, grows and reproduces. In this case, the bacterium forms a protective covering, while in the former, the cell wall is the protective covering. That, young man, is the difference between a spore and a cyst.

Thank you for your explanation. I am wondering now if in order to form an endospore a bacterial cell has to withdraw all of its contents. Bacillus anthracis has an endospore within itself. This endospore is less than the bacteria surrounding it. What is more, this bacteria is still active while having an endospore within.

A spore is the reproductive part having a protective covering as a spore for its germination has to face harsh environmental conditions such as air currents whereas cyst is the group of cells which come together to protect themselves from harsh conditions. Cyst has nothing to do with the reproduction of the cell.

Welcome to Bio. A reference would be appreciated to allow for background reading.


text:
Why do mitochondria waste energy?
In a mitochondria, it makes ATP by using energy from NADH and FADH2 electron to pump H+ into the inter-membrane space then use the ATP synthase to bring the H+ back into the matrix while using the proton motive force to create ATP.
My question here is, why does mitochondria do this, I mean, in terms of energy I think it is a waste of energy. For example using energy to put water on the top, then generating energy by making to water come down should make some unneeded energy loss.

Welcome to Biology SE! The answer to this question lies in the fact that, it would only be a waste if the mitochondria did not break even. Which it does, it uses energy to produce energy. Therefore, it isn't a waste

Thank you for your answer! What I meant to say was that, for example, let's say that you use a water power plant to make electricity. Then use that electricity(energy) to pump water high so that you can use the water power plant to make electricity(energy). Each time you do that, you lose bits of energy, until you have no energy left. In terms of physics, it's known that when you transfer energy from A to B, you cannot transfer 100% of A's energy to B. You must lose some through heat, friction or whatever.

You are picturing the system as closed one. The cell by no means is a closed system. You convert, nutrients(glucose) into energy. In your analogy, the power plant should have an external source of water providing the basic minimum to drive this pumping of water so that it can produce more energy. Then it is an almost proper analogy.

So what your saying is that, by pumping H+ in and out of the intermembrane, your creating additional energy? I don't think this true... Then, where is the extra energy coming from??

I did not say that. Take a look at this image: https://en.wikipedia.org/wiki/Cellular_respiration#/media/File:CellRespiration.svg and article https://en.wikipedia.org/wiki/Cellular_respiration#Citric_acid_cycle

@KoustavPal — Please do as it says and do not use the comment facility to answer questions.

Could you please explain in chemical / thermodynamic terms where you think energy is being wasted? When you talk about "the energy from NADH" what you mean is the Gibbs free energy change when NADH is oxidized to NAD+ in the electron transport chain. When we talk about energy being wasted in biochemical reactions we usually mean that the free energy lost in the reaction is in a form (usually as heat)  that does not benefit the cell (e.g. by the production of ATP from ADP). So, where do you think this occurs? Are you sure you don't mean why is the method of generating ATP the way it is?

I guess the OP is asking - "why pump H+ into the intermembrane space and then harvest it when H+ is on its way back. Why not directly?" This is what I could make out from the question!

This question is actually very reasonable, and your premise is not wrong.
Certainly it's true that some potential energy is wasted in the process of creating the proton gradient (when electrons are transferred from NADH to O2) and then using the proton gradient to create ATP (by ATP synthase). And you're right, it would be much more efficient to somehow link NADH oxidation to ATP synthesis more directly. Physically, this is trivially true (and it's also true for every other series of reactions).
The problem is that biochemically, it's completely unclear how to actually do this! In fact, there was an enormous mystery about this in the field for a very long time. It was known that somehow electrons were transferred to oxygen, and that this was linked to ATP synthesis, but no one knew how the energy was transferred. People postulated that there was another high energy intermediate such as ATP, but no one was able to find such a molecule. The current theory, known as the chemiosmotic theory, was proposed in 1961 and eventually won Peter Mitchell the nobel prize (https://en.wikipedia.org/wiki/Chemiosmosis#The_chemiosmotic_theory).
If you want to take the water analogy, it's as if biology just doesn't have access to a water wheel to generate energy directly from the flowing water. But it has something that can generate electricity from water falling to the ground. So it pumps up the water, uses the tools it has to generate electricity, and accepts whatever small thermodynamic loss is associated. This is a common motif -- there simply aren't biological molecules that can catalyze every single possible chemical reaction.

This answer is incorrect in accepting the poster’s premise that the two-step process wastes energy compared with a one-step process. The Gibbs free energy change for the reaction Xred +  Yox + ADP + Pi → Xox + Yred + ATP is exactly the same as if one adds in the energy change of establishing a proton gradient on the left and an extra reaction exacty reversing this on the right. There is, of course, energy lost as heat in the overall process — complete efficiency is impossible, and one needs this to drive the oxidation of NADH (as with any other reaction or reaction series).

I disagree. For instance, consider proton leak across the membrane.

I suggest that leakage per se through the lipid bilayer is insignificant, and that which does occur is regulated and used to maintain the basal metabolic rate of the organism. In any case the key question is waste, and thus whether a direct coupling mechanism would be able to convert more of the free energy to ATP. (No space to cover this in my last comment.) The problem with direct coupling is you can only release energy in ATP-size chunks — so in the real world there is a loss (the poster would call it a waste) in any case. Use of the electrochemical gradient may even be more flexible.

I don't dispute that there are other reasons why the proton gradient is incredibly useful. That would be a good alternative answer.

I may add one later in the week when I have time. But that really requires changing the question from why? to does? Some people may not like that.

Its because NADH is a powerful reducing agent. If you leave high concentrations of NADH in the cell, it would actually wreak havoc on the cell.
This is actually the reason why peroxisomes just remove FADH2s because they find no use for the extra energy and simply remove it.
So heres the simple answer. Energy is not always a good thing, because stability also matters. ATP is simply a good way to store and convert such energy.

Thank you. Now I understand. Also after reading your answer I realized that lots of enzymes and stuff needs ATP as an energy source, which means that converting all the energy to ATP(although that might lose some energy) will be easier

This is nonsense. Mitochondria do NOT waste energy in the sense the questioner implied, but was unable to explain in response to my comment. Certainly not all of the free energy change is captured as ATP, but that's no different from anaerobic glycolysis. If there is sufficient ATP in the cell this decreases the reduction of NAD by regulating the relevant  metabolic pathways.

@David what I took from the question was that why would mitochondrias not use NADH directly, as it does indeed has more free energy. Is it nonsense that NADH is a reducing agent, that it would reduce oxygens when not coupled to ATP synthesis and produce hydrogen peroxide?

First, the premise of the question is incorrect, so any answer that accepts it is nonsense. Second there is an equilibrium between NAD and NADH in cells, and the reductive power of NADH can only be used in enzyme reactions that take the reaction over the activation energy barrier that prevents spontaneous reaction. Third the conversation of chemical energy into the electro chemical potential is one of the most sublime and beautiful things in biological chemistry. An answer that regards it as a device for preventing hydrogen peroxide formation is nonsense.

So you're telling me that by pointing out what would happen in case of the questioners premise was the case, that makes it nonsense? Equilibrium shouldn't be the case since I've made it clear if it was in high concentration, which would be the case of questioner's incorrect premise. So an answer that's not practical but points out what the questioner is not seeing is nonsense? There are a lot of nonsense out there but, I don't think someone else's beauty should matter in making someone else get out of their loophole?


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

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

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

Edited to include link

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

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

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


text:
How is ATP converted to adenosine?
I am familiar with adenosine diphosphate (ADP) and adenosine triphosphate (ATP), how one relates to the other, and how each is formed in cellular respiration and photosynthesis, but I am confused as to how regular adenosine is formed.
I was reading an article on caffeine which stated:

Caffeine is structurally similar to adenosine, a neuromodulator, whose formation is dependent on the relative rates of ATP breakdown and synthesis.

From this I concluded that ATP can be changed to regular adenosine, and adenosine back to ATP, but I cannot find anything else on the internet to support my conclusion. I was also wondering when and why your body would change ADP into adenosine instead of ATP. I assume that AMP plays a role in all of this, and possibly ADA.
I only have a high school level education in biology, so please bear with me. If you do not mind, please include a source in your answer so I can further research on my own. Thanks!

Adenosine monoposphate can be converted to adenosine by a 5’-nucleotidase.

@canadianer that set me down the right track for the most part. I have one more question. Wikipedia says that ADP is converted to AMP like this: 2 ADP → ATP + AMP. What is the name of this process and where does it take place?

@CardinalSystem that reaction is called adenylate kinase and takes place in almost every living cell.

Perhaps someone could integrate these comments into a decent answer. Even the poster after he has finished his researches. I'd consider doing it myself but I know next to nothing about adenosine as neuro- signalling molecule, which seems to be the focus of this.

For a full understanding I refer you to the KEGG pathway map which is fairly comprehensive in showing all the metabolic processes that CAN produce Adenosine.
It's a bit daunting but if you find it on the map here it is interactive and you can see the enzymes and pathways involved. If you drill down it brings you to a host of papers and references in primary literature to back things up.
However the dominant process is as follows:
   2 ADP <=> ATP + AMP

enacted by an adenylate kinase then:
   AMP + H2O <=> Adenosine + phosphate

enacted by adenosine 5'-monophosphate phosphohydrolase (a 5'-Nucleotidases )

So the nucleotidase can reverse its own hydrolysis to produce AMP, and the adenylate kinase to produce ADP?

The kinase is certainly reversible with almost an equal balance of each reaction. The nucleotidase I believe is but i don't have a watertight source on it yet.


text:
Why does the right bundle branch not have any terminal filaments in the IVS of the human heart?
Dubin's "Rapid Interpretation of EKG's" briefly describes this part of human physiology but doesn't explain the reason behind it.
Is there a specific advantage of the human heart having this characteristic, or is it a flaw/useless trait?

Why is a philosophical question, but you can see, below, the most common anatomic variation, with the ventricular septum receiving terminal branches from the septal fascicle off of the left bundle branch though it can come off the common bundle. The left ventricle is larger, and as might be expected, has a greater portion of the conducting system than the right ventricle.