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How do rare mosquito borne diseases get transmitted if they are so rare?
I recently read a somewhat alarmist notice by the state board of health in NH who claimed that some man had tested positive for Jamestown Canyon virus, a rare disease even in its natural environment of Colorado. Supposedly the man has not travelled out of state.
So, I am wondering how it is possible for such a virus to be transmitted. My understanding is that a mosquito only bites twice then it breeds, so basically what has to happen is the first bite has to be on an infected human (or animal) and then the second bite on the victim. So, if this guy got Jamestown Canyon virus, then he must have been in mosquito range of some other infected creature of which we have no knowledge.
Now, unless there is some type of animal that is endemically infected with Jamestown Canyon virus which is transferable to humans, it would seem unlikely to me that there would be any source from which the man could have gotten the virus.
So, I am wondering what kind of plausible scenario would have made this disease transmission possible, assuming it really occurred?

Via Wikipedia:

The virus is transmitted in saliva to a vertebrate host when an infected mosquito takes a blood meal. It thus cycles between mosquito and vertebrate amplifier hosts, mainly white-tailed deer. In a study from Newfoundland, JCV was significantly associated with large mammals such as sheep, cattle and horses. In Michigan and Ontario moose and bison are believed to be the primary reservoir.[3]
The virus winters in mosquito eggs, which it reaches by transovarial transmission. The female mosquito lays eggs that carry the virus, and the offspring can transmit the virus to deer or ruminants and humans. Infected mosquitoes were found equally distributed throughout the state of Connecticut, irrespective of land use.[4]

So, the virus has a reservoir in (primarily) deer, an infected deer gets bitten by a female mosquito, the mosquito lays eggs with the virus, the resulting mosquitoes can spread the disease by biting another large animal or human.
The reservoir needs to be large enough to ensure the virus survives year over year, but there doesn't need to be any special mechanism for it to travel outside the predominant range; there have been cases in several states in the northeast, though rare.

References [3] and [4] are:
[3] Goff G, Whitney H, Drebot MA (2012). "Roles of host species, geographic separation, and isolation in the seroprevalence of Jamestown Canyon and snowshoe hare viruses in Newfoundland". Appl. Environ. Microbiol. 78 (18): 6734–40. doi:10.1128/AEM.01351-12. PMC 3426688. PMID 22798366.
[4] Andreadis TG, Anderson JF, Armstrong PM, Main AJ (2008). "Isolations of Jamestown Canyon virus (Bunyaviridae: Orthobunyavirus) from field-collected mosquitoes (Diptera: Culicidae) in Connecticut, USA: a ten-year analysis, 1997–2006". Vector Borne Zoonotic Dis. 8 (2): 175–88. doi:10.1089/vbz.2007.0169. PMID 18386967.


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Lipid packing defect
I have been trying to understand the phenomenon of lipid packing defect, but the resources in this subject are very limited. Well, I did find some papers, but before reading papers, I want to have some intuitive knowledge about it. Can anyone explain to me lipid packing defect in brief. Thanks

It really is your responsibility to show the research you have done before posting, give some references to this phenomenon and ask a precise question about what you do not understand. Asking someone to explain the phenomenon — whatever it is — is much too broad for the purposes of this site.

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

It would help if you could delimit in which cellular of molecular context you would like to understand packing defect, for exemple during vesicular budding or lipid droplet biogenesis.
In the larger context of cellular membranes lipid packing defect occurs when there are transient "holes" made in the phophosolipid bilayer.
These packing defects can be caused by the chemical nature of the phospholipids present in the membrane. A phospholipid is chemically defined as an amphiphilic molecule: it contains a hydrophilic head and an hydrophobic tail.
The head size can vary a lot between the different possibles groups (serine, choline, ethanolamine, etc).
The size of the hydrophobic tail which is composed of long carbon chains can vary in length (typically 16-18 carbon atoms) and saturation. The saturation is very important because insaturated lipids (16:1, 18:1) tends to have to be kinked where the insaturation is.
Thus depending on the lipid composition of the membrane, it is possible to have micro domains (previously named lipid rafts) composed of only a specific lipid or group of lipid with a defined molecular composition. Packaging defects which called be name "holes" or imperfections in the membrane might occur at the boundaries of these microdomains because of the difference of the head size, length of the fatty acid chain, and saturation.
Many people also think that proteins can be responsible for the segregation of chemically defined lipids in the membrane and cause packaging defects for exemple proteins with an hairpin structure instead of a transmembrane domain, or proteins which interact with membranes with an amphipathic helix.
I hope this helps!

source: Stack Exchange

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

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May two reactions, that share the same reactant, fire at the same moment?
I'm studying metabolic networks from a bioinformatics point of view, but I guess my question is pretty biological so I thought that maybe here I could get the best answers.
So, as the title says I was wondering, if I have one metabolite that is involved in two different reactions as reactant, is it possible that they both start at the same time at a certain point? I'm assuming that, in order to fire, the reactions need a certain amount of that metabolite, so if there is enough concentration to make both start, can the two reactions actually start in the same exact moment? What if the concentration of the metabolite is not enough to "satisfy" both?
Between the lines, are reactions mutually exclusive with respect to the shared metabolite or not?
In my mind, the quickest of the two gets the amount that it needs from the metabolite and the other one will just wait for the latter to have again enough concentration, is this intuition correct?
If you think this question is not appropriate, I will delete it and ask somewhere else. Any suggestion, also books or similar about the topic, is welcome!
I'm a computer scientist and I know just the basics of molecular biology, but I think that my job is mainly speaking to biologists in order to find solutions to different problems, so this is the reason why I chose to write here basically.

As a computer scientist, a little molecular biology is not going to help dispell your incorrect assumptions. You need to read some basic enzymology to find out how substrate concentration affects enzyme reactions and appreciate the stochastic nature of molecular interactions. Try section 8.4 of Berg et al. at NCBI Bookshelf.

What do you mean by "moment"? How big is your time interval? Usually chemical reactions are modelled as Poisson process i.e. in an infinitesimally small time interval, the probability of happening of more than one events tends to be 0. Perhaps you should read about stochasticity in chemical reactions (check out papers by Dan Gillespie). When the amount of a reactant approaches such limits that you describe, the stochastic effects dominate. These reactions can be simulated using Monte-Carlo algorithms. However, your question does not directly concern biology and is hence off-topic.

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


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How does the cardiovascular system improve upon repeated, strenuous exercise?
New here, hopefully this is the right place to post this question.
It's widely known that repeated, strenuous aerobic exercise gradually improves the capacity of one's cardiovascular system — $\text{VO}_2$ max, cardiac output, etc. The U.S. NIH, for example, states the following:

Over time, regular aerobic activity makes your heart and lungs stronger and able to work better.
When done regularly, moderate- and vigorous-intensity physical activity strengthens your heart muscle. This improves your heart's ability to pump blood to your lungs and throughout your body. As a result, more blood flows to your muscles, and oxygen levels in your blood rise.
Capillaries, your body's tiny blood vessels, also widen. This allows them to deliver more oxygen to your body and carry away waste products.

Unfortunately, I have not been able to find information about the actual biological processes that happen during repeated exercise which trigger these effects. Is it some combination of hormones? Is it a form of muscle hypertrophy of the heart?
Frankly, the subject fascinates me, and I'd be grateful if someone with knowledge about this could share it!

Regular exercise results in "increased oxygen demand," which, via the hormone epinephrine and sympathetic nervous system, stimulates the heart and, in long term, the growth of new capilaries in the muscles. Yes, heart muscle hypertrophy is also one of the results. You may want to search for something like "adaptation of circulatory system to exercise" and you'll get results like https://www.ptdirect.com/training-design/anatomy-and-physiology/chronic-cardiovascular-adaptations-to-exercise and https://www.youtube.com/watch?v=OLGy1a3w08s .

Interesting resources, @Jan — thanks for your time! :)


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Understanding presynaptic and postsynaptic inhibition
One way to classify neural inhibition is based on the inhibition being "presynaptic" or "postsynaptic".
As far as I understand, the two different types of inhibition refer to the following:

Presynaptic inhibition: A neuron N1 is inhibited "indirectly" insofar as the presynaptic excitatory neuron's action on it are dampened. This is typically achieved by neurotransmitter's impact on the presynaptic excitatory neuron which inhibit Ca2+ channels, and consequently prohibit vesicle release of neurotransmitter's into the synaptic cleft - hence the excitatory impact on neuron N1 is reduced.
Postsynaptic inhibition: A neurotransmitter acts directly on  neuron N1's receptors, leading to hyperpolarization of the membrane potential and hence a reduced probability of firing.

My questions:
(1) When we speak of "inhibitory post-synaptic potentials" (IPSPs), is this hence
always in the context of post-synaptic inhibition?
(2) I often read of "interneurons" (and it seems that this concept is used typically to refer to inhibitory neurons). Is inhibition by interneurons also always post-synaptic?

Post-synaptic vs pre-synaptic inhibition
Yes, inhibitory post-synaptic potentials (IPSPs) are always in the context of post-synaptic inhibition, because they are post-synaptic potentials. They occur because of inhibitory neurotransmitters (for example, GABA) are released and bind to post-synaptic receptors, particularly ligand-gated chloride channels. We often just call this "synaptic inhibition."
Pre-synaptic inhibition, on the other hand, would reduce the frequency/amplitude of excitatory post-synaptic potentials, by reducing neurotransmitter release at excitatory synapses (for example, glutamatergic synapses). You can also have pre-synaptic inhibition at an inhibitory synapse, where the pre-synaptic inhibition is actually disinhibitory from the perspective of the post-synaptic cell (inhibiting inhibition).
In summary: post-synaptic inhibition is reducing the rate or probability of action potentials; pre-synaptic inhibition is affecting the quantity or probability of vesicle release.
Interneurons vs inhibitory cells
Inhibitory interneurons are a major class of interneuron in the neocortex, but not all interneurons are inhibitory (layer 4 spiny stellate cells, for example, are excitatory interneurons). In addition, not all inhibitory cells are interneurons; some brain regions have inhibitory projection neurons, for example the cerebellum (Purkinje cells) or striatum (medium spiny neurons).
Inhibitory cells are those that release inhibitory neurotransmitters, so they are best thought of as involving post-synaptic inhibition. Chandalier cells in cortex are a bit of a special case, because they synapse onto axons and interfere with action potentials that way, but I would not lump them in with presynaptic inhibitory mechanisms.
Sources of pre-synaptic inhibition
In general (because there may be exceptions, and almost certainly are in invertebrates who have very "weird" nervous systems from my mammal-biased worldview), presynaptic inhibition arises from three places: autoreceptors (self receptors), retrograde signalling from post-synaptic cells, and neuromodulation. One could fill textbooks with information on all the mechanisms, but I'll give one example of each of the three types:
Autoreceptors
Glutamatergic synapses, for example, can have pre-synaptic inhibitory metabotropic glutamate receptors. These are G-protein coupled receptors, not ion channels, and they typically respond when a synapse is very active. They are effectively a brake on over-activity: if a cell is firing too much, the effect of its firing will be decreased by pre-synaptic inhibition mediated by these self-receptors. This principle is common for other neurotransmitters, too. (Wu & Saggau, 1997)
Presynaptic inhibition by post-synaptic cells
Although we think of neuronal signalling as one way, that's not entirely true. Post-synaptic cells have mechanisms to communicate with the pre-synaptic cell, and this can include inhibiting that cell.
Endocannabinoids are one mechanism: they are released by the post-synaptic cell and can reduce pre-synaptic release probability (Maejima et al 2001; Melis et al 2004). At an excitatory synapse, that makes them inhibitory; at an inhibitory synapse, they would be disinhibitory.
Pre-synaptic inhibition by neuromodulators
Pre-synaptic cells can also be affected by local concentrations of neuromodulators, like dopamine (Bamford et al 2004). Dopamine isn't necessarily released directly onto a cell but more into the surrounding area. Dopamine D2A receptors, for example, are found presynaptically at cortico-striatal synapses. Release of dopamine in the striatum reduces glutamate release at those synapses coming from cortex.

Bamford, N. S., Robinson, S., Palmiter, R. D., Joyce, J. A., Moore, C., & Meshul, C. K. (2004). Dopamine modulates release from corticostriatal terminals. Journal of Neuroscience, 24(43), 9541-9552.
Maejima, T., Hashimoto, K., Yoshida, T., Aiba, A., & Kano, M. (2001). Presynaptic inhibition caused by retrograde signal from metabotropic glutamate to cannabinoid receptors. Neuron, 31(3), 463-475.
Melis, M., Pistis, M., Perra, S., Muntoni, A. L., Pillolla, G., & Gessa, G. L. (2004). Endocannabinoids mediate presynaptic inhibition of glutamatergic transmission in rat ventral tegmental area dopamine neurons through activation of CB1 receptors. Journal of Neuroscience, 24(1), 53-62.
Nadim, F., & Bucher, D. (2014). Neuromodulation of neurons and synapses. Current opinion in neurobiology, 29, 48-56.
Wu, L. G., & Saggau, P. (1997). Presynaptic inhibition of elicited neurotransmitter release. Trends in neurosciences, 20(5), 204-212.

That was such a great answer that I took my time to read through all references. Thanks! I have a last question: Isn't a simpler presynaptic inhibitory mechanism just having the following chain of neurons: (inh neuron) --> (excitatory presynaptic neuron) --> (postsynaptic neuron). In this manner, the postsynaptic neuron is stimulated less when its presynaptic excitatory neuron is inhibited, and the presynaptic inhibition is a network effect?

@Pugl That would just be post-synaptic inhibition of the cell in the middle. It's presynaptic to the final cell that you are calling "postsynaptic", but it's post-synaptic to your inhibitory neuron. Probably the best way to distinguish would be to say that post-synaptic inhibition is referring to cases where you reduce the firing rate/firing probability of a cell; pre-synaptic inhibition is when you influence synaptic release to change the effect of a cell firing, without changing the firing rate/firing probability of the (pre-synaptic) cell.

Stated another way, post-synaptic inhibition is affecting action potentials; pre-synaptic inhibition is affecting vesicle release.

Exactly, I meant presynaptic to the final cell, thx! And that's a great and very concise definition you gave.

@Pugl I'll add it to my answer.


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Age until physical growth ceases, mammals
Fairly basic, but I am seeking a table showing how many years from birth it takes for the best-known mammals to stop growing.  (Including the latest on humans - ie. 0-17..?).

Welcome to Biology.SE!  This is a very broad question and it isn't clear what you mean by "best-known" mammals. The answer is also going to depend on environmental factors (e.g. nutrition) and what parts of the body you consider — consequently even an answer limited to humans is going to be difficult and probably not definitive. ——— Please take the time to go through the [tour] and then the help pages starting with [ask] questions effectively on this site. Thanks!

You might need to construct the table to match the conditions & assumptions you need.

I only meant what you could call gross height in humans, say.  Ie, total height!  The same for other mammals, ie, top of head from the ground.  Other hominids, apes, chimps...  Elephants ..?  Nothing too esoteric, perhaps 30 or so examples, preferably closest to humans, whether taking longer or shorter periods to fully grow than we do.


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Which species of bee or wasp are in this photo?

Please tell me what do you think :)
The photo is from Santander, Colombia. I didn’t take any closeups photos , but these were little bees, like 5 x 1 mm. The tube didn’t seem man-made, it was indoors and the owner of the house said that they are stingless, since no one has been stung.

Quick question, did you notice the bees entering and exiting the "tube", as well as entering and exiting the wall? It is common for some Halictidae species to have two entrances, one "royal" entrance, and a "worker" entrance below it. And I do find it interesting that they built a nest in a wall instead of in the ground.

If these bees are definitely stingless, they're members of the Meliponini tribe, which discounts those Halictid IDs. I'm only familiar with Nearctic Halictidae, but practically every species I'm aware of is a ground nester. The rare exceptions prefer hollow twigs, so I'm fairly confident it's not in Halictidae.
The nest entrance does appear to be consistent with a few Meliponine genera, especially Tetragonisca. Discoverlife only lists T. angustulata as appearing in Colombia, but notes that the name is applied to several undescribed congeners. A quick look at this species' nests makes me fairly confident that the bees in this photo are a Tetragonisca species.
Sadly neotropic bees like Meloponini are extremely under-researched. I'm  personally very unfamiliar with the tribe, luckily this genus in particular seems relatively well-known.

Looks like the family Halictidae to me. Known as a sweat bee. Maybe Lasioglossum zephyrus?

Could you elaborate on your what characteristics make you think of that family and why you suggested Lasioglossum zephyrus?  That species does not appear to be reported in Columbia ...


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Laurasia and Gondwana
The Cambrian explosion was 540 mya. Laurasia and Gondwana didnt collide until 330 mya. So for 210 million years the land was divided into two large continents. Plants and insects had already colonized the land long before Pangaea formed. It should therefore be possible to divide land plants and insects into two broad groups. One group that inhabited Laurasia and one group that inhabited Gondwana. I have googled around but I cant find any good info on this.

I think phrasing it as a question would help!

Is there an actual question here?


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Why is sugar absorbed very fast into the blood stream?
Recently, I heard from a pregnant person I know that immediately after she eats something sugary/sweet, the baby starts kicking and moving around, as if reacting to the sugar. She told me (unscientifically) that sugar gets absorbed fast into the bloodstream (and then into the baby), faster than protein for example, which takes a couple of hours to be digested.
However, I know that both sugar and protein must go through the digestive system until the small intestine to be absorbed into the blood. This is done through mechanical action (peristalsis), as well as chemical digestion. Yet I was wondering how there is such a big time difference between the digestion of sugars versus proteins if the path to the bloodstream is the same.
I did a little bit of research and found that there are some glucose transporters in the cheeks, which could explain how glucose is absorbed so fast (in the same way alcohol is also absorbed fast through the cheeks too).
I wanted to ask if theres any other reason or way in which sugar is given so fast to the foetus when ingested by the mother?

In short, sugars are absorbed quicker than proteins and fats because they pass through the stomach quicker and their digestion is simpler.
Sugar can be absorbed through the mouth mucosa when applied as a sublingual gel, as discussed here on Biology SE: Is sugar absorbed into the bloodstream through the walls of the mouth?, but probably in much smaller amounts during usual eating/drinking followed by swallowing.
SUGARS
Not all sugars are absorbed at the same rate.
Glucose and galactose do not need to be digested and can be quickly absorbed in the small intestine via sodium–glucose linked transporters (SGLTs) - sodium acts as a cofactor that stimulates glucose and galactose absorption (Lumen Learning).
Fructose also does not need to be digested but is absorbed much slower than glucose via GLUT5 transporters without the help of sodium (Lumen Learning).
Sucrose needs to be digested in the small intestine with the help of the enzyme sucrase to glucose and fructose, which are then absorbed. Glucose stimulates the absorption of fructose (Food and Agriculture Organization). This means that glucose and fructose from sucrose will be absorbed slower than glucose alone, but faster than just fructose alone.
Lactose needs to be digested to glucose and galactose, which prolongs the time in which they can be absorbed.
The absorption rate of various sugars is reflected in their glycemic index (the rise of blood glucose levels after ingestion): GI for glucose = 100, sucrose = 65, lactose = 46, fructose = 19.
STARCH
Starch is not digested in the stomach, so it can pass through it quickly, and is then, in the small intestine, quickly digested to glucose with the help of the enzyme amylase. The glucose from plain starch is absorbed almost as quickly as when ingested as glucose alone and faster than fructose, sucrose or lactose. This is evident from high glycemic index of foods made mainly of plain starch: cornflakes (81), instant oats (79), potatoes (78), rice porridge (78), white wheat bread (75).
FIBER
Foods high in dietary fiber slow down gastric emptying and thus absorption of nutrients (Faseb).
PROTEINS
Proteins need to be digested in the stomach by the enzyme pepsin (which slows down gastric emptying) and then further in the small intestine by peptidases into amino acids, which can be absorbed. Slow gastric emptying is the main reason for slow absorption of proteins (Diabetes Care, Experimental Physiology).
FATS
Fats are not digested in the stomach but they slow down gastric emptying, so they are absorbed slower than carbohydrates (JCEM, Vivo Colostate).
LIQUID vs SOLID MEALS
Liquid meals pass through the stomach quicker than the solid ones, so glucose from sweetened beverages will be absorbed quicker than from whole fruits (Vivo Colostate, JCEM).


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What is the name of this flower (on a tree)?
Here is a photo of a big red flower-like structure on a tree on Lama Island, close to Hong Kong. Does anyone know the name of the tree and what the black "berries" are attached to the "flower"?

I think this may be an aril or arilode rather than a flower, but I cannot be sure (see here).  If you have or can get more pictures from different angles, also some shots of the leave and bark that would be helpful.

Welcome to Biology.SE!  In addition to what @BryanHanson suggests, it could be helpful to edit your question to include size estimates for both the red flower-like and the black egg-like structures.  Thanks!


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Is the chitin in an insect's exoskeleton cross-linked?
This answer to the question How to clean and preserve a cicada's molted exoskeleton (exuvia)? states:

The exuvia is made of cross-liked chitin, and will not decay. You don't need any special preservatives as all. If you need to get the mud off, just rinse it as you said, in soapy water, let it dry, and you are done. Simple.

Wikipedia's Chitin says only:

Chitin is a modified polysaccharide that contains nitrogen; it is synthesized from units of N-acetyl-D-glucosamine (to be precise, 2-(acetylamino)-2-deoxy-D-glucose). These units form covalent β-(1→4)-linkages (like the linkages between glucose units forming cellulose). Therefore, chitin may be described as cellulose with one hydroxyl group on each monomer replaced with an acetyl amine group. This allows for increased hydrogen bonding between adjacent polymers, giving the chitin-polymer matrix increased strength.

I'm not a chemist, but "increased hydrogen bonding between adjacent polymers" doesn't sound the same as cross-linked polymers. So I would like to ask for an answer based on sources other than Wikipedia:
Question: Is the chitin in an insect's exoskeleton cross-linked? If it depends on the type of insect, then the focus should be on "a cicada's molted exoskeleton (exuvia)" as discussed in the linked answer.

I'm not sure I've tagged correctly.

Crossliking implies covalent bonds between adjacent polymer chains. I did a non-exhaustive search and it seems that there is no example of naturally crosslinked chitin. There seems to be a mention of a crosslinked protein, though.

@WYSIWYG that's my understanding as well, thanks!

much like cellulose, chitin strands are bonded to other strands by hydrogen bonds. here is a slide share with a breakdown of the structure.
It is crosslinked in the sense strands are linked to other strands in such a way that most enzymes cannot access it to break it down. this is the same thing that makes wood last untreated. In a strictly chemistry sense it is not a crosslinked polymer (which requires covalent or ionic bonding) but it still has crosslinking. Your hitting a difficulty in jargon.
source.

Thanks for the clear and sourced answer, this clears things up!

I would say that the requirement for "covalent or ionic bonding" as in the Wikipedia article is just usage of an English term that has no intrinsic chemical definition. And the difference between an ionic bond and a hydrogen bond is only a matter of degree. If the hydrogen bonds are specific (which they are) I would say that it is perfectly valid to talk about chitin being "crosslinked by hydrogen bonds". However an article on preserving dead beasties is hardly attempting chemical. I think this question would have been better on SE Chemistry and voted to close on that basis.

In polymer chemistry (and also in biochemistry) crosslinking always refers to covalent bonds (or very short covalently bonded chains) between two polymer chains.


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Can anyone please help me identify my house plant?
I know this may be an impossible task, but I am one to hope ! My mum had a house plant which had small, green, oval shaped leaves which naturally grew towards the ground (hanging plant). Once every year the plant would flower for several weeks to several months and would have little white flowers bloom. Inside the white flowers were pink baby flowers (they were tiny) and they looked like they were made of glass ! The plant did not need much maintenance and was easy to keep happy, I live in the UK.
Unfortunately my mum died last year but had given the plants to my nan for safe keeping whilst we moved house and she refused to give them back to us. I was hoping to buy one as a memento to my mum, but I cannot find it anywhere and I have no clue as to its name and I sadly do not have any photos. Can anyone help me at all please ?
Thank you,
Molly x

When you say the leaves were small, what size are you thinking of? Could you please edit your post and add an estimate in cm/inch of the leaves, flowers and the whole plant? And where the leaves rather dark or light green?

Was the white flower star shaped?

a drawing would be better. your nan can just give you an offshoot or a cutting or a photo.


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What species is this burrow-digging insect?
These are frames from a recent recording:

Location
Urban area in Central Europe.
Abiotic factors at the time of recording

Temperature = 27°
Humidity = 51%
Wind = 16 km/h

Description

Approximate size = 6 cm 4-5 cm
Elongated shape
Distinctive orange-ish abdominal segment near the end of the abdomen
6 legs
One pair of wings (I think it's very possible that it has two pairs of wings, though, hard to see on the video or pictures)

Observed behavior
The insect seemed to be digging burrows in one of my pots (so far there are 3 holes in one pot and I also saw another burrow in a second pot). Every time I've seen it, it was alone so I assume it's not a social species.
Internet search
I ran these images through google search images and the results were (in order):

hymenopteran
insect
pest
carpenter ant

I think the closest match was the first picture but I wasn't able to get a specific species so I would appreciate any insight from experts on the matter.

That is clearly a type of wasp.  Some digging leads me to think it could be something in the genus Ammophila (a type of "thread-waisted wasp") for example Ammophila sabulosa:

However, 6 cm is huge for a wasp and twice the size of Ammophila sabulosa — are you sure about that length?

The page you linked states 15 to 25mm. https://www.google.com/search?q=Ammophila+sabulosa+ruler&tbm=isch&ved=2ahUKEwiTpMiW562BAxWruCcCHR28BLgQ2-cCegQIABAA&oq=Ammophila+sabulosa+ruler&gs_lcp=CgNpbWcQAzoECCMQJzoHCAAQGBCABDoECAAQHlCxDFjQIGDRImgCcAB4AIABdIgB6wWSAQM4LjGYAQCgAQGqAQtnd3Mtd2l6LWltZ8ABAQ&sclient=img&ei=n-0EZdPYCqvxnsEPnfiSwAs&bih=580&biw=1242#imgrc=mVGVyPlWqFlclM


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General Enhancer Questions (Methylation Patterns, ect.)
I have a biological question(s) for ya'll involving enhancers.
1.) Enhancers work by being the binding sites for TFs. But how does this increase transcription? (Especially when enhancers can be extremely far away from the gene they control.)
2.) Enhancers can become methylated. When they do, does this usually prevent transcription factor binding? And if it does prevent the binding, how does this affect the role of the TF and gene expression.
EDIT:  Here's what I found.
It seems that enhancers can be far away from the gene they act upon, but the binding of TF via their DNA-binding domain can cause looping of DNA to help them reach the promoter region of the gene of interest. Thus, increasing the rate of gene expression.
On the reverse, methylation can sometimes be seen to act as silencing of gene expression. So, if our enhancer region is methylated, this may prevent TF binding and the enhancer from increasing gene expression.
BONUS:  Methylation in promoters can also cause silencing by preventing RNA polymerase II, and the required proteins (ect) from carrying transcription.
If anybody wants to add (or correct anything, let me know!)

Welcome to SE Biology. Please read the Tour and the Help on asking questions. You will see that we expect you to show evidence of the research you have done yourself to try to answer questions. What did you find on Wikipedia or other sources when you did an internet search? How did it fail to answer your question?

Thanks.. I added what I found onto my original post!  Cheers!

Your question is very broad. You can find several reviews on how methylation affects DNA function.

This subject is actually both complicated and incompletely understood. For example, there is evidence that some enhancers don't result in loops at all — instead their influence travels along the chromatin to a nearby promoter.
You can think of enhancers as being staging areas where protein complexes that promote transcription are assembled. In some cases enhancers are where the RNA polymerase complex is first bound.
When loops do form, this allows the proteins at an enhancer to interact directly with the transcriptional start site.
I think you will find this 2015 review to be a helpful introduction.1

As for methylation (which maybe would be better as a separate question), it is generally true that methylation acts to reduce transcription factor binding and thus decreases transcription.2
However, that overall trend disguises some more complex dynamics.3

References:
1: Pennacchio, L. A., Bickmore, W., Dean, A., Nobrega, M. A., & Bejerano, G. (2013). Enhancers: five essential questions. Nature Reviews Genetics, 14(4), 288.
2: Lea, A. J., Vockley, C. M., Johnston, R. A., Del Carpio, C. A., Barreiro, L. B., Reddy, T. E., & Tung, J. (2018). Genome-wide quantification of the effects of DNA methylation on human gene regulation. ELife, 7, e37513.
3: Sharifi-Zarchi, A., Gerovska, D., Adachi, K., Totonchi, M., Pezeshk, H., Taft, R. J., ... & Araúzo-Bravo, M. J. (2017). DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism. BMC genomics, 18(1), 964.


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Has anyone 'broken' an organism and then restored it to life?
Has anyone 'broken' an organism, rendering it unable to reproduce, then repaired it and observed it returned to being able to reproduce?
An example would be to restore the reproductive capacity to a cell rendered lifeless from radiation.
I've attempted, several times over many years, to find any information about this and all I've found is abiogenesis and the Miller-Urey experiment which is not the question at hand.
If there is another technical term referring to repair of life, versus creation, then I am unaware of it.
ADDENDUM: Clarified question ...limited to reproduction vs. living.

Welcome to Biology.SE! is expected that you will do some research on your own and share what you have learned when asking questions here. In addition, in a biochemical context organic refers to complex carbon containing molecules — if you got rid of those there would be very little left of an organism ...  ——— Please also take the time to take the [tour] and then the help pages starting with [Ask] questions effectively on this site. Thanks!

Ok, done. I've edited the question.

Please not that your edited-in example (which is good) does not match your first sentence: an organism that can't self-replicate anymore is still very much organic, just not alife (kind of like a virus actually).

@Nikolai So a sterile man is not a life anymore? That's kind of mean. Neuron cells are no longer alive if they don't divide?

@Cell Of course those would still be alive, I was mostly alluding to OPs example (and thinking of single celled organism for which this type of experiment might be possible). The fact that this usage of the terms oraginc/inorganic and alive/lifeless leads to wrong statements so quickly also shows, why one shouldn't use them in this context together.

Sounds to me like induced pluripotent stem cells fit your description. https://en.wikipedia.org/wiki/Induced_pluripotent_stem_cell


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Is “Oxygen-Starvation” during exercise a real phenomen?
Cross-Posted from Physical Exercise, as I suspect this Q is a bit more bio-science focussed than is appropriate for that StackExchange

I play hockey (field hockey) at a slightly-below-elite level. I train (but don't play) with players who play in the UK National Prem.
I, and other players I play with, and coaches I've trained under, have always talked about us and our brains being "oxygen-starved", when you're playing beyond your fitness level. (Especially common during pre-season when everyone's unusually un-fit :D )
What we mean by this in terms of external observable actions is that, when we get very tired we stop making good decisions, and our fine motor control drops - we chose bad passes, we take people on when we wouldn't normally do so when not tired, our hand-eye cooridnation drops so that we can no longer execute skills as well, etc. etc. etc.
Certainly the effect exist - those actions are clearly observable.
But is there truly a physiological effect behind it, and if so, is that effect truly about oxygen levels in the brain?
If one were able to install an O2 sensor in one of major arteries leading to the brain, would you be able to see actual drops in O2 levels, when someone is reaching a point of combined aerobic and anaerobic exhaustion (hockey is a heavy mix of both forms of activity, like many team sports)


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Why do birds that walk on the ground walk so "bumpy"?
Why do birds that walk on the ground walk so "bumpy"? Most other animals walk quite smooth, doesn't matter if they are mammals, reptiles or insects or walk on two, four or more legs. Birds seem to be an exception and there is no difference between flying or non-flying birds.

Related to this: https://biology.stackexchange.com/q/21200/331

If you mean the head bobbing displayed by many birds when walking: it is believed to help with visual stabilization.

The term head-bobbing, used for the apparent back and forth movement
  of the head of some birds while walking on the ground (think pigeons),
  is a bit of a misnomer. These birds don't actually bob their heads
  back and forth – instead, they move their body forward, leaving the
  head behind, then thrust their head forward past their body (hold,
  high-speed thrust!). This innate behaviour is believed to help several
  key aspects of vision during locomotion and foraging. While the head
  is still, images are stabilized on the retina and moving objects
  become clear against the background, and during the thrust phase,
  depth perception becomes more accurate.

https://jeb.biologists.org/content/jexbio/217/11/1836.1.full.pdf
In this article you can find an stroboscopic photography that shows the particular bumpy walk.

Why is it useful to birds, but no other animals, with this improved vision?

Our human eyes move a lot constantly to track movement, in the case of many birds neck mobility is probably better than eyeball mobility. Not all birds bob their heads as they walk, though.


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Is a butterfly one or two animals?
I have read somewhere that a butterfly might be two animals that combined together. One animal was a worm-like creature and the other an insect.
And the insect basically hatched inside the worm. Somehow they combined into one creature.
Is there any truth in this? Wouldn't this mean a catterpillar and a butterfly would have different DNA?
But in that case why would a butterfly lay eggs that turned into caterpillars?

Can you please provide a link to where you read this from?

From what I remember about the theories of metamorphosis, the butterfly at the worm stage just has underdeveloped wings. Basically all body parts of the butterfly are already present at worm stage.

There was a paper by: Donald I. Williamson, published in the Proceedings of the National Academy of Science (PNAS) August 28, 2009 https://doi.org/10.1073/pnas.0908357106, and communicated by Lynn Margulis.
Lynn Margulis, as a member of the National Academy of Sciences, could publish papers in PNAS without adequate peer review. Members of the academy were afforded this honor, because they have achieved the highest levels of science, and supposedly, have few peers who can review their work.
Margulis was known for her work on the origin of mitochondria from the engulfment of prokaryotes, and also the Gaia hypothesis (that the Earth is itself, a living organism). That may have predisposed her to the ludicrous idea that butterflies were the result of some strange symbiosis from onycophorans (Velvet worms).
The whole thing was a huge embarrassment to PNAS, and Margulis. It would never have been published if it had been objectively peer reviewed, and was formally rebutted as wrong, and without any merit whatsoever. See: https://blogs.scientificamerican.com/observations/controversial-caterpillar-evolution-study-formally-rebutted/

Pity cos it's quite an interesting idea even if it's not true!

Re: "Lynn Margulis, as a member of the National Academy of Sciences, could publish papers in PNAS without peer review": Do you have a source for that statement? The blog post that you link to says something quite different, namely that members could select the reviewers for peer review. (Additionally, per that post, Margulis originally made it sound like she had selected an unnecessarily large number of reviewers and then cherry-picked the few favorable reviews -- which would have been even worse -- but subsequently clarified that that was not actually the case.)

The Scientific American blog you link to is confused and positively misleading. It complains that Margulis "handpick[ed] its peer reviewers." Well, duh. That's just a heavily loaded way of describing exactly what the journal's handling editor would have done with a normal submission. Three people declining to review because they had no time is utterly irrelevant.

@zooby Look at chloroplasts and mitochondria - we're pretty sure the weird kind of symbiosis did happen there. Both still retain their own DNA (though of course, it's only a small fragment of what was there before the endosymbiosis and millions of years of evolution happened). There are also some very interesting colonies of single-celled organisms - e.g. the Portuguese man 'o war; each cell has its own DNA (they're all the same species), but is also differentiated based on its location within the colony. Looks like a potential step between colonial microorganisms and multi-cellular life :)

Good points. I added the modifier "adequate" to peer review. However, I disagree with the idea that editors always "hand pick" editors for the purpose of predicting a desired outcome. I was an editor of Systematic Biology for 15 years, and the only hand-picking I did was to ensure that they were qualified and objective.

Moths also undergo metamorphosis, so this merger would presumably have happened before the divergence between the moth and butterfly species.

@DavidRicherby the journal's handling editor is free to choose reviewers, but that is a very, very different thing to an author (or author's representative as the case may be here) chooses the reviewers. While I can suggest reviewers when I submit, that doesn't mean I get to pick them! So choosing three people who already reviewed positively and then sending the reviews to the editor is a recipe for disaster. I don't see anything wrong in the SciAm blog post.

@KarlKjer Right but "hand-picked" is just a loaded way of saying "picked". It's always "by hand".

@DavidRicherby hand-picked implies they were carefully chosen not because they were experts but because they could be relied upon to give favorable reviews. That seems like a very correct use of the term. It's supposed to be loaded since, apparently, Margulis chose folks who would say the "right thing".

@terdon I think you're confusing "cherry-picked" and "hand-picked". The latter just means chosen by a person, using their skill and judgement, as distinct from being chosen by some automatic system or process.

@DavidRicherby yes, it can mean that. But it also means selected for a special purpose.

@terdon and in addition the linked article stated that the method of publication used by Margulis will be terminated, though it was not in response to this specific incident.  This was back in 2009 so thankfully this weird system is now closed from further errors.

@zooby how to make butterfly-like creatures that are actually symbiotes of two organisms might be a viable question for [worldbuilding.se]

"Pity cos it's quite an interesting idea even if it's not true!" good for sci-fi and fantasy literature, horrible and out of place in science.

What's the definition/role of "communicated"? I guess it's similar to co-authoring.

"Communicated" means that the author contacted Dr. Margoulis, and she submitted the paper under her unique privileges as an academy member. It is not similar to co-authoring. More like sponsoring or promoting.


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What animal has fat with the highest energy density?
Fat is more energy-dense than protein and carbohydrates, it is not only an energy deposit but also an organ with many functions such as cushioning and metabolism regulations. I want to know are animal fats similar across species (composition & function), specifically what animal has fat with the highest energy density?

In both humans and animals, the body fat stores appear as triglycerides, which can be composed of different fatty acids, but they all have about 9 kilocalories per gram (USDA).
There can be different amounts of fat in different fat cells, so there can be slightly different amounts of fat in 100 grams of different types of fat tissue.
Calories in 100 g of fat from different animals:

Lard = 902
Beef tallow = 902
Chicken fat = 900
Turkey fat = 900
Goose fat = 900

The fat mentioned above was white fat, which appears as a single fat droplet in a fat cell. Humans and some animals, especially rodents and bats, also have different amounts of brown fat in which the fat cells contain a lot of mitochondria and the fat is present in multiple droplets, so, logically, brown fat tissue has lower energy density.

I wonder what the measurement error is on those estimates.


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unknown bird in Long Lake Michigan......chocolate brown head and neck, charcoal body and tail, ivory wings, top and bottom
light chocolate head and neck w/ charcoal body and tail. the wings are ivory white, top and bottom from the body outwards. the colors are clear.....not mixed with other colors. no stripes or spots, etc. slightly smaller than a robin.

Species identification questions should include a picture. It is otherwise very difficult to identify based solely on your verbal description.

Welcome to Biology.SE!  If you are unable to provide a picture it would help if you described anything else you observed.  Some examples are: behavior, calls, shape of wings, shape of beak, shape of tail, feet (webbed?) and overall body shape.

That's a very interesting set of colors.  Unfortunately nothing springs out at me, although I can think of a couple of birds that might sort of (maybe) match.
First, common pigeons come in all sorts of colors and patterns, and it's possible that yours is one.  On the other hand, common pigeons tend to be very familiar to most of us, so I don't think you'd be asking about that.
Second, there is a tern that is moving through the area about this time of year, that might fit:  Black Terns can have a lighter wing.
Here's a link and a representative photo:
 https://www.allaboutbirds.org/guide/Black_Tern/overview

There is another, even better possibility, if your bird is ternish:
The White-winged Tern (formerly White-winged Black Tern) is an uncommon late-summer wanderer through much of the region.  Here is a link and a representative photo:
https://avibirds.com/white-winged-tern/

Could it be any of these? These are all iNaturalist observations around the Long Lake, MI.


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What type of fish is this
I saw this fish in an aquarium in a nearby house .I am not sure which species and sex this fish belongs to.
[![enter image description here][1]][1]
[1]: https://i.stack.imgur.com/oOAZx.jpg

looks like a listless guppy or a platy. note the upwards pointed mouth, that is a fish that swims around most of the time and is adapted to surface feeding, they rarely stay still at the bottom. use rainwater and give them rocks and plants and they will sink less. https://www.google.com/search?q=sunset+platy&source=lnms&tbm=isch&sa=X&ved=0ahUKEwicoIK_no_kAhVJSxoKHV5yABIQ_AUIESgB&biw=1972&bih=1070#imgrc=9IXX4HlKwHCbXM:

I thought it was a gold panda molly. It looked like below [imagehttps://images.app.goo.gl/uMoAfH3o5RpF1hRk6]

Your picture is unclear. Can you please post a better image?


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How does drinking 25 mg-50mg Viagra every night cure Erectile Disfunction permanently?
https://www.webmd.com/erectile-dysfunction/news/20040513/nightly-viagra-may-restore-normal-erections#2
This article says that people taking viagra once daily can have erection restored permanently again.
Those who take viagra only when they're about to have sex do not.
I do not understand their reasoning why?
They said it helps make Endothelial cells better.
If that's the case, how come people that take viagra only when they're about to have sex do not improve?

Hmmm... I am basically asking if that research is true. Somehow you think I ask for my personal self.

I don’t see anything personal about this medical question...


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What does the final (Illumina) RNA-seq library contain? ss cdNA or ds cDNA?
I guess the oligos on Illumina's flow cell only hybridize to to single-stranded cDNAs (sscDNA).
However, when I read the TruSeq protocol (googled: TruSeq® RNASample Preparation v2 Guide) at the PCR step (AmpPCR, page 41) it looks like that the last cycle (d) is just elongation.
Therefore, since no denaturation (separation of dscDNA strands) happens, the final library input to Illumina should contain only dscDNAs which do not hybridize to flow cell's oligos!
My question is that then: when does denaturation happen? Inside Illumina? Or am I missing something?


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Why is the ability of a virus to get crystallized considered as a "Non living feature of a virus"?
My book states that the fact that :"Viruses can be crystallized" is a proof of their "Non living character"
Does that mean living things cannot be crystallized? If yes, why is that so?

Possible duplicate of Why isn't a virus "alive"?

Welcome to SE Biology. It is always necessary when quoting from sources in questions to state what the sources are. That way others can check the quotation is accurate, look at the context, and assess the credibility of the author. If you read the previous discussion of whether or not viruses are alive you will see that there is no recognized "touchstone" for life. Ability to be crystalized strikes me as one in a list of features where viruses are similar to non-living things.

Crystallization involves removing extraneous molecules, so that remaining molecules — here, virions, or virus particles — can form a crystalline or ordered structure. https://en.m.wikipedia.org/wiki/Crystallization
As far as cells go, cellular proteins can be crystallized (some more easily than others), as well as nucleic acids, but having those crystals alone is not sufficient for life. You need an input of water, energy, etc.
Making crystals from the constituent parts of cells would effectively kill that lifeform. On the other hand, you can take virus crystals, add a bit of disorder, and they will "wake up" and regain their infectious properties.
Viruses sit on a fine line of what constitutes life. To some extent, the discussion is philosophical in that definitions are chosen and the subject either meets those criteria or not, and some criteria are a bit more arbitrary than others.
Some have argued that viruses in infectious virion form are life, at the stage when infecting a cell and redirecting its machinery to make more virus particles. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2837877/
Over the decades, biology has shifted from a study of cells in Petri dishes, or monks growing peas, to a more abstracted investigation into information science and related fields and subjects: mathematics, entropy, statistics, physics. That perspective started with scientists like Schrödinger, Turing, and Von Neumann, and it continues in the modern day with work by Dawkins, England, and others.
Viruses have and continue to shape the evolution of life around them. In a way, they are frozen information, and the definition of life may be changed over time, as we gain a more broader picture of how things work.

Another minor question would be whether all viruses tolerate crystallization. Do you know anything about that? I couldn't find much through a superficial search.


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Why heart is on the left side?
I am not a biologist
but I wonder if there is any benefit for the human to have hearts on the left side?
do animals have their hearts on the left too? or on the right?

Well, it's not... it's in the center, pointing to the left side: https://biology.stackexchange.com/questions/60718/why-is-the-heart-not-in-the-middle-of-the-body https://biology.stackexchange.com/questions/5597/why-does-the-apex-of-the-human-heart-usually-point-to-the-left

There are humans with it on the right side. which side does not matter.

Possible duplicate of Why Is Most Life Symmetrical Externally But Not Internally?

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


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What type of butterfly or moth is this?
Can anyone please determine if this is a moth or butterfly and what its name? We found it near a waterfall in the Philippines. There's actually a bunch of them and it seems that it's their natural habitat which is close to the waterfall and a stream along.

That is a butterfly known as a "Mapwing". It is in the family Nymphalidae. I'm pretty sure it is Cyrestis maenalis. https://wikivividly.com/wiki/Cyrestis_maenalis

I see. Thanks you so much for the info.


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What disease does Saccharopolyspora erythraea cause?
For an examination assignment I have to find a disease caused by the bacterial species Saccharopolyspora erythraea, but I have searched the internet and have found no report of patients being infected with Saccharopolyspora erythraea. The only information I found on this bacteria is about its production of erythromycin.

I wonder whether the person setting the exam has made a mistake. For example in the paper describing the sequencing of the genome of this bacterium (Latin singular — bacteria is plural) all that is mentioned is its importance as a source of the antibiotic erythromycin.

The only mention I find for isolation of a related species in the same gents from a patient is this: https://www.ncbi.nlm.nih.gov/m/pubmed/19406809/ and it is not the cause of the disease there.

Yes sorry I meant I genus (T9 typing).

Welcome to Biology.SE!  I suggest listing the databases you have consulted — an expert might be able to help you based on knowing where you've looked either by confirming that you've searched exhaustively and that there is likely nothing to be found, or by directing to a source you might have missed.

@LazorLord. One possible source of confusion here is the change in naming and classification of micropolyspora within the family Nocardiacae, among whose species are the various nocardia responsible for 'nocardiosis'; which of itself is worthy of study.  Evidently certain members of this family are capable of arriving on Earth on meteorites.


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Why don't we have vaccination against all diseases caused by microbes?
People can be vaccinated against certain diseases. Principle of vaccination is to use live attenuated load or inactivated. My question is - why we dont have vaccination against all diseases which are caused by microbes?

We do. It says I'm due for my penumonia vaccine in some thirty years.

Imagine the stress on your immune system when you're up for a booster with 10,000 different antigens.

Mainly cost/benefit analysis. Using vaccines has a cost, both in dollars and in risk. That cost may be very low (cheap safe vaccines, like measles vaccine), or may be relatively high (smallpox vaccine is relatively risky, with around a 1 in 300,000 chance of moderate to severe side effects); but there is always some cost.
Vaccines may not have any significant benefit. I live in the urban USA; it's unlikely that an Ebola vaccine would offer me any benefit (as of the current situation in 2019). Very few people in 2019 have a significant chance of being exposed to smallpox, since it's extinct in the wild; the benefit of universal smallpox vaccine would be small.
So if the risk of a vaccine is greater than the benefit, delivering the vaccine would be more harmful than good. This calculation is done as a routine, and the vaccines people receive are known to be ones that confer more benefit than risk.
In fact, with vaccines, the benefit needs to be much higher than the risk, because with vaccines the benefit is invisible (nothing happens - you don't die of measles) while the risk is something that happens. Typically, vaccine benefit/cost ratios are very high, for that reason.
Monetary cost is also a factor. It may seem harsh to think that saving a child's life with a vaccine is given a price, but at some point the finite supply of money can be used more effectively elsewhere. If it costs a billion dollars to give a particular vaccine, and it ends up saving one life, is that the best use of money? Could it be better spent on nutrition, sanitation, etc?
This applies to quite a few diseases. There are, in academic labs and in the freezers of pharmaceutical companies, vaccines against a lot of pathogens that are not being used, because the cost is too great for the benefit. That's an equation that changes all the time; it applied to the Ebola vaccines at one point, but in the face of an Ebola outbreak those vaccines -- in those areas -- are now cost-effective.
Finally, there are a handful of pathogens for which a reasonably-priced good vaccine would certainly be cost-effective (HIV, malaria, tuberculosis, for example) but for which reasonably-priced good vaccines don't exist, because vaccines are sometimes really hard to make.

Cost-benefit also needs to look into alternative treatment options.  For example, if a bacterial infection can be treated quickly, cheaply, and with few effects by antibiotics, it needs to be extremely common for vaccination to be worthwhile.

I feel like your answer would be better if you included a disclaimer at the top in bold about how incredible small the risks of vaccines are. Currently some people may misinterpret it.

@iayork Why it is hard to make in the cases you mentioned? Using the same principles as used in other vaccinations, why we cannot make vaccine for TB, malaria, hiv etc

@AmitMaurya The problem is that a vaccine is essentially a "substance" that tricks your immune system into mounting the same response it would have to the pathogen that causes the disease. The trick is to find something similar enough to the live pathogen to represent a threat, but different enough to not cause the disease in the first place.

@AmitMaurya:  There actually are vaccinations for TB.  They aren't used in the US because they weren't effective enough (too many strains to have to cover.)  My older sister was innoculated against TB.  I'm two years younger, and by that time the TB innoculation program had stopped. I was then later exposed to TB, and have some slight damage to my lungs as a result.  It is not certain that an innoculation would have helped me.  What is certain is that innoculation interferes with the simple "tine test" for TB.  TB can be cured with antibiotics.  Detection is more important than prevention.

@Amit TB immunisation is standard practice in the UK (I had my BCG at school along with all my peers); an HIV vaccine is in the works but is non-trivial to make.

Others noted that there are vaccines for TB (old, but not extremely effective) and HIV (highly experimental, so far not very effective at all). There's also a vaccine against malaria in clinical trials. All these are good examples of my point: They are not highly effective vaccines, but the diseases are so prevalent (in certain areas) and so severe that the cost/benefit analysis might become positive even with relatively ineffective vaccines. The question of why some vaccines are hard to make at all is a separate one (which I think may be answered on this site already)

@Nathan: If the reader is too lazy to note that iayork is characterizing a 1 in 300,000 chance as "risky," then they either already believe in the anti-vax nonsense, or they were probably going to be fooled by it eventually anyway.

@Kevin I completely understand where you're coming from. But I do strongly feel that in this case, it may be better to spell it out. Some people may not understand how minuscule 1 in 300,000 is.

@akm In the case of viruses like HIV it's due to evolution - they evolve faster than we can make vaccines for them. We have lots of vaccines for AIDS and they do work but they don't work against the current generation of the virus.

@slebetman that's not correct, but it's off topic here and needs more room than is in the comments.

I would suspect that it's because not every disease caused by microbes can be treated by vaccines. For example vaccines are not as effective on microbes that cause skin infections because the antibodies generated by being vaccinated travel in the blood and some microbes damage the skin and nearby tissues without going into the circulatory system to be detected by the immune system through antibodies.
Furthermore, when bacteria reach the blood circulatory system they cause septic shock as the body responds with an inflammatory response to both the microbe and the toxins it produces, which can be fatal. But the amount of microbes that can cause sepsis is extremely diverse: bacteria (Gram negative and positive), fungi, viruses, and parasites; sometimes it happens in combination of microbes [1]. It seems impractical and inefficient to design vaccines against every microbe that cause disease because it seems that anything that can proliferate in the blood will cause disease. Microbes can even cause sepsis without going in the blood [1].
Reference:
[1] Sepsis and Septic Shock: Current Treatment Strategies and New Approaches. Gizem Polat, Rustem Anil Ugan, [...], and Zekai Halici. Eurasian J Med. 2017

Another factor that can limit the effectiveness of vaccines is antigenic variability in the pathogen — influenza viruses being a classic example, but also seen in many bacteria.

@tyersome That's a good point you can edit that in if you'd like.

@tyersome: Yeah; as I'm sure you realize, that's the same reason that people can get the flu over and over again. Another example is the malaria protozoan (Plasmodium).

Even more extreme than the flu is the common cold.  I found some research from 2016 that achieved success in animal trials, but they had to include dozens of strains in one vaccine.  And I expect that, even if this comes to humans in everyday life, it would be like the flu vaccine: a shot each year with the best guess of which strains to include that year.  https://www.nature.com/articles/ncomms12838


text:
Is there a minimum load below which an infectious agent will not cause disease?
Suppose a single smallpox virus is injected in an human adult's body. Will it cause disease in the host? Is there a minimum microbial load below which it will not cause disease?

It depends on the pathogen, delivery method, environment, etc. In most cases, a single pathogen is not enough to cause disease -- it may need many millions or billions -- but there are some cases where it does seem that a single pathogen can consistently cause infection. For example

The minimum infectious dose of ASFV in liquid was 100 [i.e 1] 50% tissue culture infectious dose (TCID50), compared with 104 TCID50 in feed. The median infectious dose was 101.0 TCID50 for liquid and 106.8 TCID50 for feed.

--Infectious Dose of African Swine Fever Virus When Consumed Naturally in Liquid or Feed
If you're asking specifically about smallpox, I don't think anyone has done the experiment (the natural and most susceptible host being humans, I think you'd have some trouble finding volunteers to find to lethal dose). A single virus of the related ectromelia (mouse pox) virus can cause death in particularly susceptible mouse strains:

The intranasal lethal mousepox model employing the A/Ncr mouse strain is used to evaluate anti-orthopoxvirus therapies. These infections mimic large droplet transmission and result in 100% mortality within 7-10 days with as little as 1 PFU [plaque-forming unit] of ectromelia virus.

--Mousepox in the C57BL/6 strain provides an improved model for evaluating anti-poxvirus therapies
As a side note, the notion of what a "single virus" actually is, is more fuzzy than you might think, but that's a more complicated question; to a rough approximation a single TCID50 or PFU can be considered to be a single virus.

According to these sources ( A, B, C, D ), infective dose varies widely among the diseases which are caused by pathogens. It is reported that as few as 10 enterohemorrhagic strains of Escherichia coli cells can cause an infection .
For an infection to occur, the pathogen must overcome and pass the physical, physiological, immunological and environmental barriers. Higher number of cells or viruses increases the possibility of overcoming these barriers. But, you should't forget that a pathogen cell or a virus particle doesn't need another one in order to infect the host, reproduce and cause a disease as a result. One single pathogen has all the necessary properties to do so.
So, in regard to the possibility of an infection, we can't say that one single pathogen can not infect a host and cause a disease. But, it is apparent that as a result of the biological properties of the pathogen and the characteristics of the infection mechanism, a particular pathogen has an observed infective dose that is different from other pathogens.
In addition to this consideration, don't confuse the number of pathogen in the environment (outside the host's body) with the number of pathogen injected into the host's body. Via the injection, the pathogen has already been transported behind some of the barriers.


text:
How can I control or anticipate the time that a caterpillar spends in its chrysalis?
My young daughter caught a caterpillar (pararge aegeria, to my non-expert eye) and we put it in a breathable jar with leaves, kept indoors in England. (Current climate is around 14-19 degrees Celcius at home, I have no specialist equipment to control the environment.)
In the last few days it has entered its pupil stage in a very dark brown chrysalis. I would like my daughter to be present at its emergence, if possible.
Is there anything I can do to either control the time that it emerges, or anticipate the time that it emerges?


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Why is it thought that protein folding is determined solely by amino acid sequence?
It seems that it is a generally accepted idea that protein folding is completely determined by the sequence of amino acids, but why do people believe that? Is it simply that no example of a protein with two different functional foldings (possibly with different functions) is known, or is there some theoretical reason that it would be impossible for such a protein to exist?

Comments are not for extended discussion; this conversation has been moved to chat.

See chat for a discussion of whether the premise of the question is valid.. that said, I think an answer can still be given (and it's okay if that answer challenges the premise), unless the community decides to vote to close.

As my comment on the question was removed I have edited the question instead to remove unnecessary and incorrect reference to principles of molecular biology, and to formulate the title in a manner that allows response by those who do not share the assumptions of the poster.

This question is, in my opinion, based on an incorrect premise but nevertheless throws up a number of points about protein folding and protein structure that can be addressed, albeit briefly.
The False Premise

“it is a generally accepted idea that protein folding is completely determined
  by the sequence of amino acids”

(My emphasis.)
No…
What is thought to determine protein folding?
The basic principle thought to be the main determinant in protein folding is thermodynamic. If possible†:

“A protein will fold so that the whole system of which it is a component is
  in the state with the lowest Gibbs Free Energy”

Thus, the protein itself is a major contributor — but not the sole contributor.
There is no argument that amino acid sequence (and composition) will be an important determinant of the contribution of the protein to the thermodynamically most favourable state, as the chemistry of the amino acid residues determine how it can interact chemically with its environment (albeit with weak interactions) and how it may interact with itself to produce a conformation which may have an appropriate effect on the entropy of the whole system.
So this is viewpoint is based primarily on chemical thermodynamic assumptions, rather than special ideas of molecular biology. An elementary exposition of this idea can be found in Berg et al. Section 1.3.4.
How can the environment affect protein folding?
One major influence is whether the protein is in an aqueous (hydrophilic) environment, like the cell cytoplasm, or a non-aqueous (hydrophobic) environment, like the cell membrane. In the former environment a protein will fold so as to expose its hydrophilic residues to the environment, in the latter its hydrophobic residues (discussed, in this paper, for example). Or it may be unable to fold at all in the wrong environment.
Another influence on the folding of a polypeptide chain may be the presence of another polypeptide chain with which it can interact, as in the case of the alpha and beta subunits of haemoglobin (see the classic paper by Perutz (1970))
Small molecules can influence the structure of a protein such as in the case of 2,3-diphosphoglycerate (2,3-BPG) on haemoglobin mentioned below.
When a protein is synthesized in an environment unconducive to correct folding it may require a chaperone protein to transport it to an appropriate environment.
And if the final structure of a protein requires covalent linkages, e.g.  between the SH groups of cysteine residues, an enzyme is need to oxidize them.
What evidence do we have for this?
We have evidence that some proteins that have been unfolded by putting them in environment that is thermodynamically unfavourable to their native (end enzymatically active) structure can refold when the environment is slowly returned to one that is favourable. This is the famous Anfinsen experiment with ribonuclease (described in this book section). Important as this experiment was in supporting the thermodynamic idea and showing that the contribution of the protein was inherent in its own composition,  it does not prove that this is what happens in vivo, nor that the structure formed is the one with the lowest thermodynamic free energy.
The importance of individual amino acids in the sequence is attested by examples such as the mutation of a single amino acid in beta-globin in sickle-cell anaemia (glutamic acid to valine). Under certain circumstances this allows the haemoglobin molecules to polymerize into long fibres because of the interaction of the hydrophobic valine residues with residues in  another subunit rather than with water.
Different states of folding are possible in a single protein
This addresses the section of the question regarding a possible:

…example of a protein with two different functional foldings

There are many so-called allosteric proteins that are regulated by interaction with small molecules (their environment) which cause a shift from one conformation to another. The example par excellence is haemoglobin, which is in an equilibrium between two states that are influence by the binding of oxygen, hydrogen ions (i.e. the acidity of the blood) and 2,3-BPG.
Another type of example is the shift that can occur between the secondary structures producing amyloid proteins.
†Can we be sure that a protein always adopts the structure of the lowest energy?
No.
The manner in which a random coil is a highly complex field, but, in brief, one can imagine that the path to the structure of lowest energy is blocked in some way (an energy barrier that would have to be overcome, perhaps) so that the structure adopted is, instead, the lowest attainable in practice.

[A rugged energy landscape with hills, traps and energy barriers and some narrow throughway paths to native — from Dill & Chan, 1997]

IMO this answer is self-contradictory. The highlighted statement 'A protein will fold ...' is in fact the Anfinsin position. To quote from his Nobel lecture: "...the  three-dimensional  structure  of  a  native protein in  its  normal  physiological  milieu  (solvent,  pH,  ionic  strength ..)  is  the  one  in  which  the  Gibbs  free  energy  of  the whole  system is lowest;  that  is,  that  the  native  conformation  is  determined  by  the  totality  of interatomic interactions  and  hence  by  the  amino  acid  sequence,  in  a given environment" and is  not a 'false premise'

@user1136 — I am answering the poster's question and his assumption, not discussing Anfinen's Nobel lecture. As for your thoughts on VSGs, I suggest that you incorporate them into an answer of your own. As a comment on my answer they seem to have no place.

@user1136 the answer does not contradict itself, and you even pointed out why. It is a false premise to assume that the conformation is totally determined by the sequence. It is true that the conformation is determined by the sequence AND the environment (at least for an instant; disordered regions don't adopt a stable conformation), assuming that 'environment' also accounts for post-translational modifications.


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Cactus plant identification
I received this cactus as a gift and I'd love to know the family/scientific name. Only one flower has bloomed since, it was between orange and yellow. At first it was perfectly spherical, but in one month it has become almost pear-shaped.

Welcome to Biology.SE! Please edit your post to include an uploaded image. ——— Links are discouraged since 1) if they break they render this post and any answers worthless, and 2) they can be used to link to malicious websites. Thanks!

Thank you tyersome, uploaded a new image!

You're welcome — that seems like an unusual shape for a cactus, but at least it's happy!  ——— You might find this website helpful for figuring out your new friend's identity ...


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Software to model and analyse protein–ligand interactions
I am currently trying to model a certain protein (Golgi Mannosidase II) and compare the induced fit of the inhibitor swainsonine. I would like to be able to analyse the distances between bonding interactions and the strengths of bonding regions. I was wondering if there was any type of software that would allow me to analyse this protein and its interactions with swainsonine? I have seen many images like the one below in research papers, but I’m never sure what software the researchers are using to generate these models.

Liberato, M. V. et al. Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism. Sci. Rep. 6, 23473; doi: 10.1038/srep23473 (2016).

This appears to be a bioinformatics question rather than one about biology.

I know it is rather dense, but the methods section of the paper you cite indicates how the simulations were performed. If you search this site you will find a number of other questions about straight protein molecular modelling software.

I don't know precisely what you mean by "analyze", which could be anything from simply "view" or "measure distances", to evaluating an energy function on a crystal structure or molecular dynamics simulation, to prediction of binding sites de novo. The tools are different for each case, though some can do several things.
For simply viewing, measuring distances, and creating "pretty pictures" like the ones you included with the question, PyMOL and UCSF Chimera are the most popular tools. Chimera is highly scriptable and can perform molecular dynamics simulations (i.e. simulate movement of atoms based on an energy function), though its capability in this regard is somewhat limited. The NAMD/VMD software suite (which was used in the study cited in the question) is more full-featured, as is CHARMM (the latter of which is also the name of an energy function). For prediction of binding sites de novo (without a bound experimental structure), i.e. "docking", there are DOCK and AutoDock (both with long academic histories) as well as more industry-oriented ones like Glide.
Be careful though what you're getting into — while simply viewing structures and making geometric statements by direct observation is well within reach of the average biochemist with reasonable knowledge of protein structure (provided you trust the lab that solved the structure in the first place!), simulation of proteins using energy functions requires considerable computational expertise, though the "black box" nature of some software glosses over this. It may be relatively easy to run a simulation using questionably appropriate parameters, but the adage "garbage in garbage out" applies very much here. This is somewhat true with docking as well.

+1 for the last paragraph alone

A good answer, but be careful about statements of which tools are most popular. You do not mention Jmol, which is one of the viewers available on PDB and is quite powerful. Also, you could enhance your answer with links to the software.

I have edited your answer to add that the NAMD method was used in the study cited in the question. You can revert my edit if you wish, but improving questions and answers is a valid part of the SE model (although should be used with care).

I'm not an expert but a start could be PyMOL https://pymol.org/2/
Unfortunately, you need a license to use the latest version
An earlier (free) version can be found here:https://sourceforge.net/projects/pymol/files/latest/download
A tutorial can be found here:https://pymolwiki.org/index.php/Practical_Pymol_for_Beginners
Hope that helps to start!


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What is the chemical structure of myosin?
What is the chemical structure of myosin? Specfically, what functional groups or monomers are they made of?

What have you already learned in searching?

I just know the functions and the categories of it.:( Based on the research, I know that it is a motor protein and acts with actin to perform muscle contraction. Also that some types of myosin performs other  activities like phagocytosis or transporting vesicles  and that there are powered by ATP hydrolysis. I only have basic knowledge of chem and bio but I assume that since it is a protein it is made of amino methyl or carboxyl groups.

Ok. Why do you want to know the chemical structure? What will it tell you? With proteins, we don't usually talk in terms of chemical structure, but as chains of amino acids. Really you should probably learn more about amino acids first based on your comment.

Thank you for the reply. I'm  doing a project related to macromolecules, and for me it is myosin.  The thing that concerns me is that there is one part asking about the chemical structure (functional groups ,monomer, and polar regions). I researched and read some article for hours. I understand how it functions and impacts the body but I could't really grasp  how it is chemically made and I feel like I'm lost:(  This sounds like a stupid question but would you mind recommending me how to approach this kind of research, like what concepts I could know for better understanding?

Probably the Wikipedia pages on proteins and amino acids would help you - you probably also have a textbook with similarly helpful descriptions. You kind of need to understand those basics before trying to understand the structure of a particular protein.


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Parasite? or a possible home infestation?

I found this bug on my bed tonight.  It's smaller than a sesame seed. 6 legs and 2 antenna.
Is this causing my dog and I to itch? Should I be concerned?

It is a minute pirate bug, in the family Anthocoridae. https://en.wikipedia.org/wiki/Anthocoridae They are generally thought to be beneficial insects, in that they are predators of pests. Do you have some house plants that may be infested with something else they are feeding on (like aphids)? Unfortunately, minute pirate bugs do bite, and the bite is painful. https://hortnews.extension.iastate.edu/2017/10/minute-pirate-bugs-are-biting-argh
But these are not human parasites, and I would not be concerned. Just find what they are feeding on, and take care of that.


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Length at which a branch 'branches'?

An image from this question (and originally from Karl Niklas' computer model) has prompted the following question:
The branches in this tree divide with increasing frequency as we progress from the bottom of the tree. This clearly makes sense from the perspective of light absorption efficiency and is a phenomenon I have often observed in real trees. The model in question created trees for optimal light favourability, stability and reproductive ability (in this case just light favourability). What other factors affect the length at which a branch splits or produces an offshoot? How does this initial sprouting determine the 'final' shape of the tree's branches.
DISCLAIMER: appreciate that perhaps this question is too broad - my initial interest in the specific subject was from a more mathematical standpoint (I am a physicist). I am simply seeking a more biological/complete explanation to the phenomena.


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What could humans do to "see" what dogs smell?
We're able to see a lot of things using computers that we can't see normally: yellow-green, UV light, X-rays, etc. What do we have that harnesses the ability to "see" what dogs smell (e.g., harnessing a dog's sense of smell to detect cancer and so forth)?

Welcome to SE Biology. Please re-read the Tour to see why your question is not appropriate here: "Focus on questions about an actual problem you have faced. Include details about what you have tried and exactly what you are trying to do. Ask about... general questions about biological concepts, questions about the biological mechanisms behind medical conditions, questions about techniques in a biological or biochemical laboratory" and "Avoid questions that are primarily opinion-based, or that are likely to generate discussion rather than answers."

@David Is it truly opinion-based? I'm asking for actual methods of being able to perceive senses that are outside of our natural abilities in the same way that we perceive sound and sight when they are outside of our immediate knowledge.

RoCo I believe your question is a valid one and fits on our site. However, please indicate what previous research you've done (e.g., Google, Google Scholar, web of science, the library, etc.) and what you've already found out (or not found). Our goal is not to simply be an answer site, but rather a site that promotes self-learning with some expert help along the way :). Please take a moment to edit your post with this additional detail, and it will likely be received more positively by our community. Thanks!

In addition to my original point and that made by @theforestecologist I would have voted to close your question on two other grounds. First it was too broad, it didn’t focus on one specific problem such as odour detection of a particular disease, and second it concerns the technology of odour detection devices, rather than biology. As they say, please read the label before use.

NMR spectroscopy is a technology that is used to identify molecules. So-called "NMR spectra catalogs" document the spectra of various known compounds. Acquiring these spectra requires purified samples, expensive equipment, and time. In addition to making next-generations of this technology into something that would be practical for realtime "smelling", you'd have to match up catalog entries with what dogs actually respond to. That's going to take a fair bit of work.
There's some literature online about growing olfactory sensory neurons in a Petri dish (with difficulty). If we can learn how the signaling pathways work for "odorant detection" for specific odorants or "fragrances" that we already know dogs perceive, perhaps we could genetically engineer a cultured neuron cell to "light up" a fluorescent marker or issue some other signal that is perceptible to humans, whenever some dog-specific odor wafts in. I suspect this would be more realistic than "tabletop NMR" in our lifetime.

Warwick University's e-nose technology has been around for quite a while: https://warwick.ac.uk/fac/sci/eng/research/impact/electronicnose/
As far as I understand their technology, they sample gas, and analyse it using a solid state CMOS device to generate a signature signal for particular compounds/mixtures.  The devices have been used in a variety of industrial gas sensing applications.
There has been some progress in using e-noses in medical diagnosis, for instance this paper reports the use of e-noses to sample volatile organic compounds from urine in type 2 diabetes diagnosis: https://www.ncbi.nlm.nih.gov/pubmed/30513787
The difference from NMR is that e-noses don't generally try to identify specific molecules, but rather, to generate a signature for a particular organic compound or complex mixture, which can then be compared with other signatures from other samples using a machine-learning approach.


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What species is this? What the fruit?

The berries of the fruit are sweet. The tree is growing in Israel.

Please edit your post to include where this tree was growing  — for identification questions it is important (and often essential) that you include location information.  Pictures of the bark could also be helpful.

@tyersome I added bark

This does look somewhat similar to a mulberry though I agree it doesn't look right for a white mulberry.  I would, however, guess that it is something in the Moraceae (Mulberry family). —— To test this you could break a small branch or tear a leaf — plants in this family produce latex (a milky looking sap) when damaged.

@tyersome after thinking about this, I agree.

Is this a street/landscape tree?  What town?  Jerusalem has a detailed tree inventory if you read Hebrew.

@Bryan Hanson yes it is street (planted) tree in a park. It is in Haifa.

Unfortunately I can't locate a street tree inventory for Haifa.  And street trees are frequently not native, which expands the range of possibilities. Your pictures are great, someone will surely know this tree but I cannot figure it out.

@tyersome I tested for white sap and there was none.

Well that's confusing!  Maybe Haifa has an urban forestry department (or something similar) that might have someone who can answer this?  If you do get an answer, please share it here.

Looks like it is Phytolacca dioica.  I found this by searching your first image in a phone app called Pl@ntNet (PlantNet).  Looking at Wikipedia confirms the ID.
Interestingly, you said the fruit was sweet.  The North American relative Phytolacca americana is extremely poisonous.  A brief search suggests your species is possibly poisonous, with reports about the leaves more common than the fruit.

This site says the berries are juicy so can reduce thristyness: http://travelermap.ru/chudesa-prirody-13/

Good to know!  Another interesting difference is that your specimen's berries are yellow-green, while P. americana has intensely red-purple berries, due to betalain pigments.  Glad we figured this one out!

Phytolacca esculenta also has black berries but it is edible and cultivated. The difference between this and american variety is the form of the berries. Also, dioica is a tree while the other two are not.

Perhaps a white mulberry? See the Wikipedia: https://en.wikipedia.org/wiki/Morus_alba

Of course, not. The berries are of totally different size and the leaves are totally different.


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flavivirus virus genome, methylated guanine
I'm looking at the sequence of a flavivirus virus genome (mRNA). Kindly see the link MH900227.1. How can I identify the Guanine nucleotide that is methylated in the capping process?
Thanks,

You might give us a link to the sequence you are looking at. If it is a GenBank file the annotation might help. You might also tell us what relevant papers you have retrieved from the literature that discuss the topic and why they don't help you. See the Help on Asking Good Questions.

I've added the like to the sequence. I think it's a general question for biologist/virologist so I did not ask the authors.

What else do you know about this sequence? How was it generated? A quick blast search suggests that it is not a complete sequence and that it is missing the 5' end — do you have some reason to believe that this is a complete genome sequence? ——— Also, are you familiar with how 5' capping occurs — if not looking into that may help you better formulate your question.

Hi tyersome, The cap (GpppA) should be at the 5' end. However, the mRNA deposited in database showed different nucleotides in the 5' end. I did Blast search for all mRNA sequences available but it shows no (GA) in the beginning of the sequence. Since there are serveral "GA" nucleotides in the sequence , I wrote my question about how to identify the guanine that is in the cap and will be methylated in the capping process. Here is the other sequences of mRNA LQ868304.1  LQ868303.1 LQ868302.1 LQ868301.1 LQ868300.1 LQ868299.1

Why do you think the methylated G is present in these sequences?

I have two reasons for thinking your question isn't answerable.

As I said in my comment, based on BLAST results I don't think your sequence is complete — it appears to be missing the 5' end.
If the 5' end is missing then the end that gets capped is missing.

The 5' cap gets added post-transcriptionally and has a linkage (5′–5′ triphosphate) that prevents it from being sequenced.
That means that sequencing reaction don't see the G that gets methylated in the 5' cap.
This is why I suggest that you make sure you understand the capping process.

Thank you tyersome for your reply. (1) for the first reason, you are right. I updated the link in the question to a sequence which should be a complete one . (2) for the second reason, I suppose that the 5' cap will appear in the sequence, even-though if it added post-transcriptionally, in case the mRNA was directly isolated from the bacteria and not from the DNA. Please correct me if I 'm wrong.

I encourage you to make sure you understand how sequencing reactions work.  If you review that and look at the structure of the 5' cap I think you will understand my second point. (You could also look at the sequences of a few eukaryotic mRNAs — you will find that they don't always start with a G.)

That's a bit extreme. Ask yourself, how did they ever identify and characterize mRNA caps? The review I cite in my answer indicates there is a capped mRNA (Figure 1).

Question

“How can I identify the Guanine nucleotide that is methylated in the capping process?”

Answer

Not from the genome sequence MH900227.1 mentioned in the question. It is the sequence of the genomic RNA (given as DNA), it starts with an A and even the full Genbank entry lacks any annotation of whether there is a separate capped mRNA and, if so, where it starts.

To answer your question you will have to search the literature. There is a 2018 review by Göertz et al. entitled Functional RNA during Zika virus infection which should have (or lead to) the answer. It does appear from Figure 1 of that review that Zika virus polyprotein mRNA is capped, although the position is not immediately apparent just skimming the paper. Some hours of work and access to a university library is probably required to track it down.


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Can prawns and lobsters live out of water for more than six hours?
I live in Telangana which is a state of India.I like eating Non-vegetarian food.People of our state eat pond fish more comparing to other aquafood.In many places near me,I've seen people cutting alive fishes in to pieces with their big knives.I won't feel good to see this.So,usually I bring the pond fishes home and keep them aside for atleast 40 minutes with no water in contact to them.In these 40 minutes I prepare other ingredients needed for the recipe.After these 40 minutes,generally as there is no response from those fishes I start cutting them into pieces.In the same way I don't know how much time it will take for prawns and lobsters to die without water.Do they live more than six hours without water?
This question is not related to the experiments carried out by the biologists on lab creatures.They are great people.I encourage their experiments whether it involves humane killing or inhumane killing because their experiments on one creature may help millions of remaining creatures.

TL;DR version is they are gill breathers and need to be in a humid and moist environment to have a considerable longer life span outside sea water.
Dr. Cowan's on being asked the same question about lobster said:

“Gills work best in seawater, but if lobsters are kept in containers of seawater with no aeration, they quickly use up the oxygen and suffocate,” she said. “That it why it is imperative to transport lobsters in containers with no standing water.” - New York Times

Many lobsters, shrimps and even crayfish & crabs are transported in boxes with a small amount of water in the bottom and they survive for several days like that. However the long term side effects of this are still to be discovered as most crustaceans transported this way get cooked.


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Why doesn't chloride cause high blood pressure?
Assuming osmotic pressure is the (main?) culprit, why isn't the chlorine ion loose in your body after eating salt considered equally responsible for hypertension?
I have searched Google and Wikipedia, and cannot find an answer.
I have looked here at Stack Exchange, too.
Why is it that you always hear about how bad 'sodium' is for your diet, but every sodium cation comes with a chloride....
Could someone point me to an article, at least?

I made an important change to your title: chlorine -> chloride. The latter is the anion in salt, which is presumably what you're interested in. The former may cause high blood pressure via a horrific death.

what have you done to answer this question? this will inform community on how to help you

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

Not every sodium comes with a chloride ion.  For instance sodium bicarbonate (baking soda), sodium nitrate (in preserved meats), monosodium glutamate (Chinese food), and many more that are used in food (or sometimes medicines).

Boy, so many people are obsessed with how much OPs research..

Osmotic pressure is not the main mechanism of sodium-induced high blood pressure.

high dietary salt raises cerebrospinal fluid [Na(+)]. This leads, via the Na(+)-sensing circumventricular organs of the brain, to increased sympathetic nerve activity (SNA), a major trigger of vasoconstriction

How NaCl raises blood pressure: a new paradigm for the pathogenesis of salt-dependent hypertension.