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Does one wing of fly contain harmful microbes and the other contain only antibodies?
There was this study but the conclusion and it's source's relability seemed a bit off. How come a house flies one wing contain all microbe and the other don't.

In addition to @S Pr's answer, what would possibly be an evolutionary reason for flies to "care" what the microbes on their bodies do?  Seems much more likely that the presence of microbes on flies is purely accidental: they just stick to the fly's feet & mouthparts when the fly feeds.

Curiously, there is interest and research on how microbes and microbiota affect feeding, courting/sexual fitness and aggregation. Microbes also can alter social communication in Drosophila. Whether or not flies care or do anything about it is not yet abundantly clear, but there is a clear relation between microbes and Drosophila emerging in recent years. So the question is really interesting; the paper liked by OP is the exact opposite of what is interesting in the field!

I really think this question should be closed because the function of this site is not to review papers. Any question here should be about a biological problem and comprehensible on its own. The poster perpetuates the (imho) nonsense of the author by talking about fly antibodies. INSECTS DO NOT PRODUCE ANTIBODIES.

That's one of the weirdest science pubs I've ever seen, starting with reference to a 1400 year old hadith, and it's difficult to read because it's not very logical. Let's not forget that the same hadiths say that the moon and heavens followed at the same time. In reality, the moon came 9 billion years after the heavens, so a book that is wrong by 9 billion years in scientific terms shouldn't be cited as modern science facts.

Does one wing of fly contain harmful microbes and the other contain
only antibodies?

False.
A healthy microdose of skepticism is all you would ever need here. It's just a silly attempt to prove a literal interpretation of a religious text with minimal effort.
Unfortunately, the paper looks, reads, and smells like a joke. Ignoring its nonsensical title and its unintelligible sentences, it is most clearly a rather transparent attempt at indoctrination and evangelism. It is a very dirty attempt to disguise ideology as science. It does this so poorly however, that both honest laymen and honest scientists would be able to spot it within a few seconds of looking at the paper.
It is absent of properly carried out science, but it does look like a phoney mock-up of it. The "biology" contained within is completely laughable, I'm sorry to say. One example of it is the pretend experiment with an n of 1, its lack of controls, and its method section that doesn't indicate anything pertinent. Something about the use of a microscope, but an appeal to simply looking at the tubes which are photographed under some very funny backgrounds and lighting.
Personally I don't recognize the journal, it seems that it may be a fake/predatory journal, and it has been discountinued in Scopus in 2014 for whatever reason. My favorite parts? The research question:

The aim of this research was to clarify the miracle in the   hadeeth
of   the   prophet   Muhammad   (PBUH)   by studying the antimicrobial
effect of the fly wings. And to understand this aspect from the
scientific point of view.

And the grand conclusion at the end of the discussion:

Also  this  information  has  not  been  discovered  only a  few
years  ago.  this  speech  testifies  the  honesty  of  our prophet
(PBUH)band also it contain a replay to any one claiming  that  the
talks  of  prophet  are  full  of  myths moreover every word uttered
by him is right from God the almighty

I would gladly replicate this experiment for you (and the original author), it would hardly take two minutes of work (separating wings from 4 flies)... but I don't know if it would even be worth the time for any other reason than pure entertainment. This is obvious fraud and I post this answer only because the hilarity of the "paper" inspired me to. I have never stumbled onto this kind of research before, it's... perspective-building to say the least.
PS. I checked the ORCID of the author, I can find no publications that they claim to have published in journals, except for what you can find on ResearchGate. Most of the links are false links. Claims also to be a world academic champion in 2017 in microbiology (veterinary medicine), whatever that means. Claims to be a professor at Shaqra University. Can't find them on the official staff list of the university. Also, self-described:

She is the World Academic Championship 2017 in microbiology and she
was recognized as among World's 500 Most Influential Experts in
Microbiology for the Year 2017 on Earth according to International
Agency for Standards and Ratings

Hilarious!
PSS. Found a correspondence address to the author where they seems to have photoshopped some of their 'work' onto a blank journal page with formatting. I will ask the author on your behalf and let you know what they think of your question. I hope for a swift reply!

what about this paper ?  I know it sound weird for me to ask this questions but ı see a lot of papers like this. @S Pr

Nope, it's all religious zealotry. No scientific basis. I guarantee you that if i were to replicate the experiment, and falsify the results, the original authors would not accept the null hypothesis (that their religious verses are evidently falsifiable myths). That would be the honest test. Scientific papers look very different and are more rigorous. I see you are very new to scientific literature. Perhaps have a browse and see how good peer-reviewed science even looks; a simple bar chart is really not enough for any argument to hold.


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Medical Physiology
I've come across the topic of the influence of inhaled ammonia (caustic ammonia) on breathing rate and some cardiovascular changes. All of this stuff is thought to be mediated through the fifth cranial nerve (CNV). I found some articles about:
(1) https://www.ncbi.nlm.nih.gov/books/NBK11036/
(2) https://journals.physiology.org/doi/abs/10.1152/ajplegacy.1928.87.2.319
but the key point here is the scheme of reflex. Are there any articles or textbooks, that contain an explanation of such phenomena from a neurophysiological point of view? Thanks.

Possibly better suited to medical science stack.

Please [edit] your post to have a descriptive title that includes your actual question, not an extremely broad category.

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Identify orange-brown, teardrop-shaped insect in central Europe that was found indoors
TL;DR Can someone identify the species of the insect in below picture? Editing of the wording of this question (if possible) to make it easier to find by using search engines is welcome.
I caught this insect and was wondering what species it was:

Here a milimeter-scale and an USB-plug next to it to allow to estimate the size (sorry that they are so unsharp but I hope it is sufficient to get the size):

I was not able to find it by reverse image search or by searching for some keywords using google. I also checked some questions here but did not find any that seems to be about such an insect.
Following description/keywords are added to help someone searching for such an insect to find this using word-search. If someone can formulate this more search-engine-friendly to make this more likely to be found, please edit or add a comment so I can edit it:

Teardrop-shaped
six legs / 6 legs
two antennas / 2 antennas
orange-brown / brown-orange
size about 3mm / 3 millimeters / 0.11811 in / 0.11811 inches (I hope my calculation from mm to in is correct)
if touched by glas or paper, it remained motionless for about 1 to 2 minutes
no wings / not airbourne / walking
able to walk up walls
it was found indoors
the region is central Europe

Many Thanks in Advance.

For everyone who may be waiting for an answer to this or who at some point in the future find this through google: I have found the species fo the respective insect, it is Gibbium psylloides (https://en.wikipedia.org/wiki/Gibbium_psylloides).

Thank you for posting an answer to your own question. Please note that you are much more likely to get a positive response to your answer if you explain why your identification is correct. Specifically, please [edit] your answer to add discussion of key features that led you to this conclusion and supporting references or at least validated images. Without this your answer is indistinguishable from opinion. ——— Please consult the [help] pages for additional advice on [Answer] effectively on this site.

I think it may have been a tick of some kind, one that had already fed and was round (hungry ticks are sort of flat).  I couldn't say exactly what species.
I'm not sure, but that's the only thing I can think of that matches this photo.  I'm no professional, so another person here may be able to do better.
Ticks have eight legs (they're vaguely related to mites, and, even more distantly, to spiders), so I was puzzled at first by you saying it had six legs, but possibly what you thought were its antennae were its other pair of legs?  (Ticks have no antennae).
https://en.wikipedia.org/wiki/Tick

Thanks for the answer. I see the similarity with tigs but I doubt this is a tick. For onc, I think it really had antennae because it moved them while walking instead of using them as legs. In addition, ticks would likely not remain motionless if touched because they have to grab prey walking past them when sitting in the gras. Also, ticks have their legs somehow streched out to the side, this one has them kind of V-shaped. I agree that from the general description this could be a tick so this answer may be good for someone else finding this through google. Please note that I did NOT downvote.

Fair enough!  Thanks for the comments, that makes sense.

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Does transcription terminate at the end of antibiotic resistance genes on the Duet expression plasmids?
I am working with the pETDuet and pRSFDuet plasmids to express RNAs under control of the T7 promoter. On these plasmids the antibiotic resistance genes (Amp for pET, and Kan for pRSF) are downstream of the T7 promoter site where I cloned in my genes. The Amp and Kan genes are transcribed in the opposite orientation of the T7 promoter and since these genes are downstream from where I inserted my genes, readthrough transcription from the resistance genes would result in a sequence complementary to the RNA sequence I wish to produce. My question is: do the antibiotic resistance genes in these plasmids have a built in transcription termination mechanism?
I have used the ARNold tool: http://rssf.i2bc.paris-saclay.fr/toolbox/arnold/index.php to look for Rho-independent terminators at the 3' end of the antibiotic resistance genes and in the region downstream. There was one hit for the pETDuet plasmid but nothing for the pRSFDuet plasmid. There were no hits for the  pCDFDuet or pCOLADuet plasmids either. My sense is hairpin terminators were not specifically incorporated to stop transcription downstream of the antibiotic resistance genes. The other possibility is the antibiotic resistance genes terminate in a Rho-dependent manner, is this known to occur for the Amp and Kan genes?

Generally they do, however this is often doesn't completely stop transcription run-through.
Note that in a T-7 reaction there shouldn't be any transcription of the Amp or Kan genes as these are run off promoters that  the T7 phage RNA polymerase won't be able to transcribe off as it is extremely specific for the T7 promoter.
The solution if you are really worried is to linearize your plasmid immediately downstream of your terminator but before the AMPR gene using a restriction enzyme with a single cut. This will also give you a specific size sequence being transcribed, which is very useful if you are determining copy number in say a qPCR.


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Is it possible to produce a tangible mass of DNA/RNA using a PCR reaction?
A Polymerase Chain Reaction (PCR) is a method of amplification which enables one to produce many copies of a certain DNA/RNA strand for many applications (as described in the link above).
I have never seen the actual process and the resulting PCR solution, but according to Wikipedia, the volume of the solution is of the micro- to milliliter magnitude.
I was wondering: if this process were allowed to continue on and on, while supplying all necessary nucleotides and other materials, to the magnitude of, say, liters - could we end up with a tangible mass of DNA/RNA? In other words, will we be able to extract from the solution a solid mass of DNA/RNA that is visible to the naked eye? If yes, can we predict the physical characteristics of such mass?

PCR amplifies only DNA not RNA.
A PCR reaction is typically within the  micro liter volume, and can go down to the nano liter volume for qPCR. The maximum volume of a PCR tube is 200 microliters. The maximum volume a 96 well thermocycler can handle per well is usually 100 microliters. So the maximum amount of reagent volume one thermocycler can handle at a time us 9.6ml
I have never seen anybody scale a PCR to mili liter volume, as that would be rather expensive and excessive.
However if some some reason, somebody did do as you say, yes it is possible to obtain visible quantities of DNA. (Removal of impurities would be required first... ie unreacted dNTP, primers) And given that we can obtain visible quantities of DNA by extracting DNA from bacteria or salmon sperm.. I am sure a chemist somewhere would be able predict the physical properties of that DNA mass.

PCR on a milliliter scale can be useful e.g. for use as a template for large-scale in vitro RNA transcription. It's not the most common use for PCR, though.

Presumably, if we were to go through N PCR cycles and start with a few dozen litres of solution, I don't see any reason why there's be a limit to the amount of DNA PCR can produce. The limitation is only in the size of the machines available in the market, not in the underlying chemistry.

aside from machine limits, other limits are also present.. pyrophosphophate (PP) that produced went dNTP are polymerised is an inhibitor to polymerase enzyme.. Repeated heating will cause deamination of cytosine to form uracil.

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Does using animal models for medical research also promote veterinary research on these animal types?
I have been reading about mouse models for studying inflammatory bowel diseases such as Crohn's disease and Ulverative Colitis. For example, according to this publication, a widely used mouse model for colitis is the Dextran Sulfate Sodium (DSS)-Induced Colitis.
This got me thinking: when we induce disease in mice (or monkeys, fish etc.), is that somehow beneficial for veterinary research of these animals when they get sick (unrelated to medical research focusing on humans)? Are the data from pre-clinical trials used for that purpose in any way?

Short answer is no. Human disease take a long time to develop naturally, far longer than the lifespan of animals models used (mice, rats or fish).
Also the cost of the drugs far exceed the cost of the animal. There is little point in spending $40k to make a non-commercial anti cancer drug to save the life of a pet mouse who has developed the rare cancer.
Longer answer... some... a bit. Not quite what you expect. There are a few labs that are re purposing anti cancer drugs that failed animal (mouse) trials to treat dogs. It appears that people are willing to spend a fair amount on experimental drugs to save the life of the family dog.
Mice have increasingly been shown to be a poor model for human anti cancer drugs. Their cells grow to fast, their immune system is subtly different from humans. Stuff that work in mice often times are too toxic in human or just don't work. A longer lived animal model is needed. However dogs as experimental animals is too costly to maintain, too much red tape to use and takes too long for cancer progression (You cannot wait 2 years for a cancer experiment to finish).
However a sick family dog with cancer is another matter.

I don't follow the logic of this answer - it seems focused on the usefulness of animal models for human disease. It hardly addresses the actual question about veterinary research.

The animal models used (in research) are too short lived to be naturally affected by many of human disease that are being researched. So direct application of this research to mouse health care is very limited. Furthermore when using said research data is used on human, often we find the work not applicable. So by guess work successful mouse anticancer drugs are unlikely to be successful in other animals either. The best use of research in mice has been the use of failed (by mouse test) anti cancer drugs in pet dogs.


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How do metal ions acting as enzyme cofactors "find" their respective enzymes?
Metalloproteins are metal-dependent proteins, i.e. they require certain metal ions (copper, magnesium, zinc, etc.) for their correct function in the body. Since proteins are manufactured inside cells by the ribosomes and metal ions are exogenous materials, i.e. are obtained from food, how would a metalloprotein and its respective metal ion find each other in the body? Are the metal ions taken inside all body cells? Does the meeting take place in the blood?
A quick Google search retrieved nothing useful.

The metal ions are transported across cell membranes by various mecanisms like channels, pumps or extracellular receptors for carrier protein.
The loading step mostly happens in the cell. Once transported inside, some ions just diffuse into their binding site on the protein; others, like iron, need a scaffold.
Some essential enzymes are metalloproteins, for example most ATP-using enzymes need magnesium; and the respiratory chain needs iron. Thus most cells will have transporters for these metal ions.


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Gene products of recessive/mutated alleles
I probably would not cite a specific example, but some recessive allele work by encoding for the non-functional form of an enzyme. While the dominant allele encodes for sufficient levels of functional enzyme that the dominant phenotype is present in heterozygous individuals. Will the individual have many uselessly non-functional proteins floating around along with everything else?

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Sex of fern gametophytes
The following image is from Campbell Biology, 12th edition

It says, "Each gametophyte develops sperm-producing organs called antheridia and egg-producing organs called archegonia". This seems to suggest gametophytes are either always hermaphrodites or most of the times hermaphrodites.
I have done a little bit of searching and now am convinced that they are not always hermaphrodites.

"Most ferns, on the other hand, are homosporous; they produce a single
type of spore. After germination, each fern spore has the potential to
develop into a male, female, or hermaphrodite gametophyte."

https://science.sciencemag.org/content/346/6208/423.summary#:~:text=Most%20ferns%2C%20on%20the%20other,%2C%20female%2C%20or%20hermaphrodite%20gametophyte.
Are they most of the time hermaphrodites? How common are unisexual gametophytes?

Your image has text (top) that reads "most fern species produce a single type of spore that develops into a bisexual photosynthetic gametophyte." So right in that source, you know already that no one is claiming that they are always bisexual (by which they seem to mean hermaphrodites), and a statement that they are both hermaphrodites. I do not see any conflict between the textbook and the quote, and the textbook at least seems to think that they are mostly hermaphrodites. Generally, making  statements with the word "always" is a bad idea in biology.

@MaximilianPress There is a contradiction.
a) Most fern species are hermaphrodite
b) Most fern species have the potential to become  a male, female or a hermaphrodite.
a) and b) are potentially contradictory.
My question was about the ratio. what is Male:Female:Hermaphrodite gametophytes? The answer will depend of the species ofcourse. So can be a complicated. But It can be easy too, for example Overwhelming majorities of gametophytes may be hermaphrodite

I do not see that your statements (a) and (b) are contradictory. Obviously the implication is that unisexual gametophytes are relatively rare, as you suggest. I am not a fern biologist so I don't know about relative proportions, but measurements of these proportions have been done in at least some species, e.g. https://www.jstor.org/stable/23728097?seq=1, which do show slight majorities of bisexual gametophytes in the lab and in the field.


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Why do we spend so much time on creating taxonomies?
I spent 3 years building a taxonomic database of plant specimens for the Missouri Botanical Gardens (http://www.tropicos.org/). Myself and two other programmers used a modern database and web pages to share the specimens with the research community. Last I looked there are over 3 million specimens included. Anyway I never got a straight answer as to why there is so much time, money and botanist's lives spent categorizing the earth's flora. What is the end goal here? I'm hoping there are professional scientists here that do taxonomic work that can chime in. Thanks.

Your question is too discussion oriented for the stackexchange format. The answer invariably will be "it depends whom you ask." I suggest looking at the broader impacts section of the grant that supported your work, which should answer the question "why does this matter?".

I think this is a legitimate question. I am not a taxonomist but certainly one reason is to understand life species relatedness and their evolution. Why is that necessary? Well I guess the main goal here is to fully characterize our ecosystem but more precisely, and as an example, when a biologist starts to work on an organism knowing to whom he is related is a precious starting information as one might expect similarities between very close species (i.e. use previous research perform in that close relative to drive studies in the new organism).

Interesting, that makes sense. One of the other suggestions I had heard is that if they find a plant specimen closely related to a rare specimen that can cure an illness, the closely related specimen may deliver the same medicinal qualities.

I agree with kmm. Why do we spend so much time compiling and tabulating Baseball Statistics? Why did we spend so much time figuring out the nature of light, gases, metals, radioactivity, toxicity, bugs? Why in fact do anything other that chase after herds of elks and dig for roots and berries. Oh but wait, you need knowledge to know which ones are poisonous and which ones will provide you with additional calories when the hunters have had a bad time of it.

You have asked a question with the bias of "This is useless, prove me wrong." It would be a more reasonable question if you said "I am a programmer who worked on a taxonomic problem for 3 years but I did not get an understanding of the relevance of the work. I would like to gain a better understanding of the benefits, uses, and values to producing such taxonomical archives and are there shortfalls to this mode of study of natural systems."

Biology is about observation and learning from nature. If you categorize the species, it helps you in quickly understand what the species is about, what are some of its common characteristics, phylogenetics, etc. It has applications not just in understanding evolution, but in population studies, ecology. Why do we give humans names? So we can find them quickly and easily and associate them with certain characteristics. It is the basic human nature of using patterns to quickly identify objects.


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Is Berlin patient immune to HIV after bone marrow transplant?
Is the Berlin patient here : https://biology.stackexchange.com/a/39364 become immune to HIV after bone marrow transplant? Or in other words: Can he get HIV infection again?


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Do animals with crypsis know where they should stay to save their lives?
For example, would a green lizard know it need to stay on a leaf, and avoid creeping on ground? Or in general, would animals with crypsis know what color they are and then hide on suitable place? Or they don't planned to do it and just be unlucky if they leave their suitable place and be seen by predators?

Is there any reason you are particularly interested in consciousness in animals that hide and not consciousness in general? Do you expect an answer that is any different from an answer to the question "Are animals conscious?" (Relevant: Wikipedia > Animal Consciousness)

@Remi.B I think this is not only about consciousness but also about awareness and perception.

I am not sure there is any commonly accepted difference between consciousness and awarness. At least I don't get the difference. It seems important that the OP make sure to define the relevant terms and explain why the question "Are animals conscious?"  would differ from the current one.

I think you can break this down into two sub-questions:

Will natural selection select animals whose crypsis and behavior align with each other? The answer here is definitely yes, but with a few caveats:

Crypsis might not be the best strategy in a particular situation: a green lizard crawling on a leaf might be outcompeted with a red-and-blue lizard that is poisonous, for instance.
Either behavior or crypsis might be easier to change over evolutionary time: you might see your green lizard evolving to spend more time in leaves (particularly if it's herbivorous or eats plant-dwelling insects), or you might see it evolving brown pigmentation to hide on the ground.
Natural selection isn't going to be concerned with individual actions but overall behavior. So a lizard might fall off a bush, get spotted on the ground and eaten. But it might dash from bush to bush without getting caught. But if a lizard spends most of its time on leaves, there might be selection towards it being well-camouflaged on leaves.

Does this require a conscious decision on the animal's part? I think the answer here is no, consciousness isn't necessary. Very simple animals show responses to their environment, such as bacteria swimming towards food. Your green lizard might be staying close to leaves that it feeds on, or near the insects it feeds on that itself feed on the leaves, and so stay near the green leaves that camouflage it by accident. Or its brain might be programmed to carry out a complex action to hide it better. Perhaps the most sophisticated examples of this is animals that reconfigure their body to match their surroundings, such as octopuses, cuttlefish (but not, interestingly enough, chameleons!)
This doesn't mean that the animals don't have consciousness or are not deliberately hiding by finding surroundings that match themselves. It just means that that's not necessary to explain why we find green lizards hanging out on leaves.


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Can HIV be automatically cured by waiting until CD4 T cells count drop to 0?
As I know, HIV needs host cell, CD4 T cell to repicate itself, and at late stage of AIDS, count of this cell in patient will drop to 0, my question is, if we can provide a sterilised environment for AIDS patients at late stage, will HIV be cured because CD4 T cells drop to 0 and hence no host cell for HIV to replicate itself?

Short answer: no. You might be able to put the patient into a sterile environment, but they will always carry into that environment every normal and - worse - opportunistic - organism they have into the room with them. So, no. They will die from bacteria or reactivated viruses or fungi or parasites (e.g. toxoplasmosis) that live in the body.

HIV can hide in many kinds of immune cells, like macrophages.


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Can saltwater fishes survive in sugar solution?
I know saltwater fishes can't survive in freshwater because of osmosis that water would rush into the body of fishes. How about sugar solution? Does sugar solution provide similar conditions as salt water for saltwater fishes?

No, the chloride cells in the gills rely on the relationship  between chloride and sodium to remove salts out of the body against the gradient. Switching the environment to sugar would cause the chloride cells to not be able to maintain ionic regulation. See the below link for basic info on chloride cells: https://en.m.wikipedia.org/wiki/Chloride_cell


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Can stem cells from male convert to cells of female-only organs, and vice versa?
As we know, stem cells can convert to different cells of other organs, can male use their own stem cells to convert it into cells of female-only organs(and vice versa)?

Well a stem cell is what every cell comes from, they go through differentiation to become any cell in the body. So theoretically, yeah that kind of differentiation could occur, you'd just need the correct stimulation.

@user19270 no, you are completely incorrect. There is no "stimulation" to change an X chromosome into a Y, or vice versa.

I am assuming you are talking about embryological stem cells and embryological development of genitalia.
The answer is no.
Male stem cells have XY chromosomes. Y chromosome is the sex determining chromosome with SRY gene that determines testes development. Absence of the Y chromosome leads to female development by default. That is why XX forms women and there are people with only one X chromosome which are women. (Turner's syndrome)
It might be possible that SRY gene undergoes a mutation and the gene isn't expressed. There are Y chromosome linked diseases.
You should read up about Y chromosome and development of genitalia.
https://en.wikipedia.org/wiki/Y_chromosome
https://en.wikipedia.org/wiki/Development_of_the_reproductive_system


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hummingbird feeders - is sugar water healthy for them?
The top results on google for DIY hummingbird feeder suggest a white-sugar solution for the feed.  In humans we make a big deal about processed sugar vs. the sugar you get from, say, eating a piece of fruit.  Does this matter for hummingbirds?  Their metabolisms so high, it makes me wonder if this is relevant.  Maybe it is not!  But I would like to know.

It is likely especially the lack of nutrients in sugar water that is present in honey that will be deleterious. Just like feeding ducks bread impacts health negatively, because there's nothing of use in there for them.

You should only use white sugar. Anything else (honey, brown sugar etc) can harm them. Hummingbirds get their nutrition from bugs. Lots and lots of bugs.

@AliceD I think a more accurate statement would be "no trace chemicals", since the carbohydrates in both foods are extremely useful to animals.

@Pungh0li0 The first half of the statement is unsupported, and the second half is patently false (hummingbirds subsist on nectar, not insects).

Here's a relevant study showing (Anna's) hummingbirds lost weight but had no behavioral changes eating nothing but sugar water for 10 days. Obviously in the wild hummingbirds will have access to much more than just your hummingbird feeder. I'm sure it also varies with species. http://www.sciencedirect.com/science/article/pii/0300962992906435

@CactusWoman Is 10 days long enough?

@MarchHo I thought that hummingbirds only ate nectar too, but a quick google search informed me that insects are part of their diet too.

@GoodGravy Thanks for the correction and TIL.

Hummingbirds absolutely eat insects, and HONEY and BROWN SUGAR are a huge NO NO.
  The following is a statement from: http://wildbirdsonline.com/index.html

Every year, as more studies are completed, we learn more about
  hummingbird life and diets. However, we find that some people think
  that hummers can survive on nectar alone. Nectar provides quick energy
  to sustain their extremely high metabolic rate and little else. This
  is important enough that the shape of the bills of hummers have
  evolved in partnership with the flower shapes that they frequent.
  Consequentially, there is a wide variety of hummingbird bill lengths
  and shapes among the more than 300 species that exist.
There is another critical food source for the hummers. Essential
  vitamins, minerals, amino acids, proteins, oils and fats, fiber, etc.
  all come from the insects they eagerly consume, not the nectar. Their
  preferred insects include, but are not limited to: small beetles, true
  bugs, weevils, flies, gnats, mosquitoes, aphids, mites, leafhoppers,
  flying ants, and parasitic wasps. Their favorite insect food source is
  the spider and harvestmen (daddy long legs). Some ornithologists
  estimate that spiders are between 60% and 80% of their diet.

But there are lots of other resources for you to find accurate information about feeding hummingbirds.

Hummingbirds eat nectar, which is a high sugar solution. You're assuming that they'll eat sugar water instead of insects.I would assume the sugar water feeders act as a substitute for nectar, and the humming birds will prey on insects all the same.  Is there any evidence for this either way?

Also, why is brown sugar such a big no-no (genuinely interested, not rhetorical)?


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Genome Sequencing
Is Genome sequencing used to determine the relationship between two species that are believed to have a common line of descent? How accurate is this method if so?
Are there more accurate methods for determining if two species have a common line of descent?

Yes, genome sequencing is one of the least subjective means used to infer common descent. It is still to some degree subjective, because we target specific parts of the genome that we think are useful - e.g. either conserved or variable across species.
It is impossible to say how accurate this method is, because we do not know the truth. We have no reference value. It is impossible to determine (i.e. prove) the relationship between species unless we observe the speciation; we can merely collect evidence that supports or refutes a theory of common descent.
There is a fairly comprehensive page on Wikipedia that describes the various types of Evidence of common descent.


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Genetics of Hybrids

I'm working on this problem, but I'm not sure I've done it correctly. My initial thought was that the answer was $D$, but I don't see anything in the above graph that indicated the Hybrid species is,in fact, less fit for survival. Moreover, I cannot see why any of $A,B,C$ would need hold.

The number of off springs produced by the Generation 0 and 4 is almost the same in case of Hybrids. This indicates that the rate of production in the Hybrids is almost the same among different generations.In this case option D will be the best one to choose.


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Blebbistatin effect on vesicles
Blebbistatin is a drug that specifically inhibits the assembly of myosin in the cytoskeleton. What effect would you expect blebbistatin to have on intracellular vesicles?
The formation of vesicles would cease.
The movement of vesicles within the cell would cease.
The vesicle membranes would fail and release their contents into the cytoplasm.
The vesicles would be unable to fuse with the plasma membrane.

I don't readily see how Blebbistatin would effect intracellular vesicles; I believe this ignorance comes from not knowing what myosin is and how it interacts in the cytoskeleton.

What textbook are you reading from?

Blebbistatin inhibits myosin II by blocking it's attachment with actin. Myosin II and other actin based motors have shown to be involved in vesicle budding from trans golgi network. Given this information, I think correct answer will be

The formation of vesicles would cease.

Following cartoon from (Stow et al 1998) shows proposed mechanism,

However looking at this paper, option (2) The movement of vesicles within the cell would cease, also sounds reasonable.

Option 2 is correct. Vesicles do not need cytoskeleton for their formation (it is dependent on, among others, structural proteins like COP-I/II and clathirin).

@WYSIWYG: Kinesins and dyneins do transport vesicles, and are not affected by blebbistatin. www.ncbi.nlm.nih.gov/books/NBK21710/

Blebbistatin blocks effectively the Myosin II light chain kinase (MLCK)activity, and myosin being a motor protein, plays an important role in vesicle traffciking thereby affecting the process of endo and exocytosis.
With this information, I think it would be logical to say that blebbistatin will cease the formation of vesicles, the vesicle movement and inturn will inhibit the ability to fuse with the plasma membrane.
It looks to me more like a cumulative effect of blebbistatin on the intracellular vesicles.

Vesicle formation would not be inhibited.


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Is the ringing sound in the ears caused by dying ear cells?
I was recently watching the movie "Children of Men" (great movie) by Alfonso Cuarón. Now in a certain scene, the lead actor happens to be nearby a loud explosion. Later, when he complains about the 'ringing-sound' in his ears due to the explosion, a co-actor replies:

Julian: You know that ringing in your ears? That 'eeeeeeeeee'?    That's the sound of the ear cells dying, like their swan song. Once it's gone you'll never hear that frequency again. Enjoy it while it lasts.

How true is that statement?
Do the ear-cells really die after such an incident?Can you really never hear that frequency of the ringing-sound again?

Welcome to Biology. The statement maybe true dependent on the loudness of the explosion. In turn depending on the power of the explosion and the distance od the listener to the sound source.

Short answer:
That MAY be the sound of the damaged hairs dying. You MAY not hear that frequency again but that's unlikely.
Long answer:
Okay, so tinnitus, or ringing in the ears, can happen because of many reasons. There are three real kinds:
1) Spontaneous tinnitus can happen because of slight shifts in the acoustic systems of the ears, some of the hairs in the cochlea may amplify wrong and create a tiny feedback loop and ring for no reason. see this article about that kind of tinnitus here
However, that's not the kind of tinnitus you're referencing. That kind, post acoustic trauma, is more serious.  This kind (which can result in hearing loss) results from either 2) one really loud noise OR 3) prolonged repetitive exposure to certain frequencies (like how your mom told you to turn your headphones down or you'd go deaf. Lower frequencies move a lot of air and can indeed be dangerous to your hearing.) Just how serious the damage from a single acoustic trauma event like the explosion from Children of Man would be to you would depend on just how loud the noise was you were exposed to, the frequencies of it, and how close you were.
So now that we've gone over the different kinds of ringing-in-the-ears (tinnitus), we can talk about how it works in this situation.
This is a great article on acoustic trauma tinnitus.
So these characters didn't rupture their eardrums or they'd be in a lot of pain and unable to hear at all in one side. Instead what happened was the tiny hairs that send electrical signals to the brain were probably bent and crushed (see awesome images on the article above of before, at, and ten days after acoustic trauma.) Three possibilities from here: either the hairs recover, they partially recover, or they don't recover at all. The most likely situation is that they do recover in a matter of days, leaving the characters with undamaged hearing. Some of the hairs (usually lower frequencies) may be more damaged that others. Those may dim or cut out frequency ranges in hearing. Multiple hairs cover the same range, so some of them may be out of commission while others survive, leaving you with diminished hearing of that frequency. However, that is not likely to be related to the buzzing/ringing frequency we first hear after acoustic trama, which is the sound of all damaged hairs freaking out and sending signals at once.
Great article on how we hear frequencies
source: Sound engineer. Protect your ears, guys!


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Can radiation therapy cause cancer?
Radiation therapy is a very popular cancer treatment method. But can it have any risk for make a different cancer? Because i think that radiation exposure can make DNA mutation and thus increase the risk to cause cancer, so why we still use radiation to treat cancer? That's so contradictory.

Yup. Radiation induced secondary cancers exist and vary in their site of incidence and risk of incidence based on the site of treatment. In breast cancers treated with radiation, for example , there is upto a 3 fold increase in relative risk relative to the general population for leukaemias within five years and 1.5 times the relative risk for secondary lung cancers within 15 years.
The literature also reports 1 in 10 malignancies as being of a secondary nature, and radiotherapy amongst others is probably responsible for a fraction of those.
Despite this risk, radiotherapy is very often worth using because without it the risk of dying from the primary cancer is vastly greater than the risk of a secondary malignancy from therapy, and secondly, unlike systemic chemotherapy, the side effect profiles of radiation are more tolerable and localised.
It is also possible to "shape" fields of irradiation to maximise the dose delivered to the tumour and to minimise exposure to normal tissue; this is called intensity modulated radiotherapy (IMRT).
Also, a lot of the cancers radiotherapy is used for occur in older people, and the benefits of saving someone from their primary tumour again outweighs the risk of secondary malignancies later on. It is especially of concern in paediatric patients because that brings with it the risk of secondary malignancies in middle-age, but advances in intensity modulation I think has the potential to minimise that risk.


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Is there no good way to run the Vienna RNA tools on Windows?
I'm trying to get the Vienna RNA tools (particularly RNAfold) running locally (as opposed to using the web interface--because I have lots of sequences I wish to process in batch mode). On the website, it mentions that there are pre-compiled versions of the software available for all major operating systems, however the site seems to be down. All that's still accessible is the GitHub page with source code access.
From my experience, trying to get large C/C++ projects, that often have quite a few third party dependencies, to compile is a huge pain. And even the Python "version" (really a Python wrapper around the C++ code) doesn't install with pip, despite having a compiler available (and found by pip), there are quite some header files that aren't on my Windows system that it complains about--and I've generally never had a problem with pip not being able to install other Python packages, even ones that are internally mostly C/C++. Even installing Anaconda, then bioconda, and then trying to install "viennarna", it isn't found. I'm beginning to think that these tools are just broken other than on the sorts of workstations on which they were developed, which already have all the necessary dependencies and headers.
Has anyone else managed to get a local install of these tools working?

It think this question is ways better fitted for the bioinformatics community: https://bioinformatics.stackexchange.com/ Shall I migrate it?

I can access the website normally, and I have been using precompiled ViennaRNA on Windows without any problems.

@Chris I didn't know there was a separate bioinformatics community, yes it would be better migrated there.

Against my better nature (I think that this is a question about software, not biology), I offer:
https://www.tbi.univie.ac.at/RNA/#download

This download works for me to get the precompiled packages.
You could also try here (for a few days): davidleader.net/Wienershnitzel/index.html

I have edited the answer to remove the irrelevant pieces Domen is responding to.

And so we are left with the situation that a helpful and correct answer to a question, despite being off-topic, is sitting on -1. And all because I pointed out that most modern bioinformatics is written on and for Unix-type operating systems, which does not include MS Windows but does include another which also has widespread support for consumer software.

That website gives a time out error for me, and has been doing so all week. In fact all of tbi.univie.ac.at is inaccessible for me, not just /RNA or the download page. I can access the Github no problem since it's a separate site but the download links from there only lead back to that site.
If it works for you, then it must be an internet problem outside the site itself.

@biohacker I can also access the page. Unsure what the issue is on your end, I am looking on Firefox. Possibly switch browsers? If the download were smaller, I would simply link you to a version hosted elsewhere.

@biohacker I was using Safari on the Mac, which sometimes has trouble because of Chromocentric websites. Where are you trying to access from? North Korea? I’m in Britain.

@biohacker I wonder if you're on a network where someone has a bit over-aggressively limited which URLs are accessible, perhaps assuming that domains that are not ".com", ".edu", etc, must be hosting sketchy sites.

I'm on Chrome, in the United States. I can access univie.ac.at (which takes me to the main university home page) but not tbi.univie.ac.at. I will try accessing from other locations, but I believe I've tried also at home (where I'm not behind any sort of filter) instead of at work without success. I did manage to find Ivo Hofacker's faculty page by searching starting from the main university homepage, but it doesn't seem to have a link to the software.

@biohacker — I'll download again and mount it on a webpage for download.

@biohacker Try https://davidleader.net/Wienershnitzel/index.html

@David Thanks for that!

Another few options: run Vienna on a virtual machine with a (totally free) installation of linux - basic ones like Ubuntu or Mint are very easy to install. Run on a Linux distro designed to run from USB drives - Puppy linux used to be the goto there, dual boot a linux distro, or (best IMO) run one of the several docker containers for viennaRNA .


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Optimal Growing Conditions concerning CO2 level (ppm) for aquatic plants
I know this is rather specific but I would like to know what level of CO2 concentration in the water is optimal for the highest possible plant growth rate.
I did an experiment where the growth rate increased with higher CO2 levels in the water of the plants. The highest ppm were 60 but I don't know if higher levels would keep increasing plant growth or decline due to high acidity of the water.
The specific plant if this helps would be limnophila sessiliflora
Any information on this would be much appreciated.
Jonas

have you tried Google Scholar yet ... ? it looks like some plants also use HCO3- ... https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/j.1469-8137.1981.tb03198.x


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What other sites do non-competitive inhibitors bind to apart from allosteric sites?
I learned competitive inhibition and non-competitive inhibition.
My teacher told me that we should say that non-competitive inhibitors bind to somewhere on the enzyme apart from active sites.
I thought 'somewhere on the enzyme apart from active sites' refers to allosteric site. Because allosteric means changing shape and non-competitive inhibitors do change the tertiary structure of enzymes. However my teacher said this is wrong -- non-competitive inhibitors do bind to allosteric sites but they also bind to some other sites as long as they don't bind to active sites.
So, I am wondering, apart from allosteric sites, where else can non-competitive bind to? Or, is my teacher wrong?

I think your teacher is more than a little mixed up. A competitive inhibitor, for example, can bind to an allosteric site (and not to the active site at all): all that is required is that the binding of the inhibitor prevents the substrate from binding to the active site. See part (e) of this diagram, for example.  My thoughts on such issues are recorded here, and I won't rehash them. But IH Segel is excellent on (reversible) enz inhibition (quoted in the above ref)

The fact that a competitive inhibitor need not at all resemble the structure of the substrate is one of the things that so impressed Monod

Does this answer your question? Identifying type of inhibitor from $K_m$ and $V_{max}$

@user338907 that is an answer! Very well done.

Here is a helpful excerpt from the lecture notes for Introduction to Molecular and Cellular Biology at Columbia University, taught by Lawrence Chasin and Deborah Mowshowitz (emphasis mine):

Re: noncompetitive vs. allosteric inhibition: noncompetitive inhibitors bind to a site other than the active site and render the enzyme ineffective. Allosteric inhibitors do the same thing. So, how are they different? And, in what way can we apply the Michaelis-Menton equation to our understanding of allosteric inhibitors? For instance, can we quantify what happens with the presence of an allosteric inhibitor, or do we just have a qualitative understanding?

I agree that at a simple mechanistic level non-competitive and allosteric inhibition appear the same. There are several differences, however. Allosteric inhibition generally acts by switching the enzyme between two alternative states, an active form and an inactive form. It usually works by binding to a sites in a specialized subunit of a mutimeric protein, and thus binds at several sites. The more inhibitor that binds, the more then can bind, and vice versa with substrate. The kinetics are thus complicated, being cooperative, and non-Michaelis Menton, and are beyond the scope of this course. So a qualitative understanding is all that is called for here. Allosteric inhibition is designed into the proteins and represents an important physiological process.
Noncompetitive inhibiton is more of a catch-all for non-physiological inhibition that does not compete with substrate for substrate binding to enzyme. In that, it is defined (and named) from a negative point of view. As described in your texts, a non-competive inhibitor may bind to a non-substrate site on a protein and distort it to the point of non-functionality, and adding more substrate will not alleviate this inhibition. Or, as in the example I used in lecture, it may simply block a catalytic site without interfering with substrate binding, an example that is more distinct from allosteric inhibition.

In addition, note that an allosteric inhibitor may display alternative kinetics in reference to substrate binding, as described in this NIH guide:

An allosteric inhibitor decreases activity by binding to an allosteric site, other than or in addition to the active site on the target. This interaction is characterized by a conformational change in the target enzyme that is required for inhibition. These conformational changes can affect the formation of the usual enzyme-substrate active site complex, stabilization of the transition state, or reduce the ability to lower the activation energy of catalysis. Figure 1e and Figure 2a are classical examples of allosteric inhibition. As such, an allosteric inhibitor may display a competitive, noncompetitive, or uncompetitive phenotype with respect to substrate binding.

(+1) I think the first part of your answer and the last part are using two very different definitions of 'non-competitive inhibition'. The NIH site (which I agree with) distinguishes between competitive, uncompetitive and non-competitive inhibition. C and Mowshowitz seem to be unaware of uncompetitive inhibition and use the term 'non-competitive in a  archaic way to cover everything that is not competitive. But even working within the (correct) NIH definition, there is a problem:  what Cleland and his school refer to as 'non-competitive', European kineticists tend to call 'mixed inhibition'

For Cleland, see Enzyme Kinetics and Mechanism

I hate to sound naive, but I always thought that the active site of an enzyme encompassed both the substrate-binding site and the catalytic residues. So if an agent inhibits an enzyme by irreversibly chemically modifying a catalytic residue, it would seem to be both non-competitive and acting at the active site. Of coarse it is crass stupidity teaching this stuff about inhibitors to school children (and most undergraduates) when the emphasis should be teaching them what we know about catalysis and it’s regulation.  I prefer to talk about poisons and regulators.

@David couldn't agree more. Putting hard semantic borders around scientific concepts often just leads to confusion when students (inevitably) find exceptions to the definitions. An archetypal question on this site seems to be "My professor said X is the case, but my textbook argues Y. What's true?"

@user338907 it seems you have thought this through more than I have. Indeed, this is a concept that I've always found a tad confusing myself. My personal understanding of allosteric regulation has always been that allosteric factors tend to be endogenously-produced regulators with concomitant sites for activity, whereas "noncompetitive" regulators can be exogenous factors or poisons. Though my understanding certainly has its flaws

@David I think the terms 'competitive, uncompetitive, and non-competitive refer to reversible inhibitors. But of course, an irreversible inhibitor  may give rise to a Lineweaver-Burk plot that looks 'strictly' non-competitive (a plot such as this) because irreversibly killing the enz could give rise to a LB plot where both the slope and y-intercept is changed to the same extent (ie no apparent change in Km) , for the reasons that you give. Kineticsts (used to) delight in pointing this one out!

To try and 'tease out' the non-competitive/mixed inhibitor confusion.  (All of the following refers to reversible inhibition). Let's analyze the types of inhibition by the patterns produced on Lineweaver-Burk (1/v vs 1/s) plots: (i) A competitive inhibitor affects the slope but not the y-intercept (no effect on Vmax) (ii) An uncompetitive inhibitor affects the y-intercept but not the slope.  So far so good ...

(iii) The Europeans refer to the situation where both the slope and intercept are changed to different extents as 'mixed' (reversible) inhibition and the 'special' case where both the slope and y-intercept are changed to the same extent as 'non-competitive' inhibition. The LB plots will intersect on the x-axis (see here, for example). (iv) But Cleland  refers to all cases where both the intercept and slope are changed as 'non-competitive' inhibition and the case where both are changed to the same extent merely as a special case)


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Why doesn't the cell just use one messenger?
I recently learned the second messenger model, where adrenaline activates adenyl cyclase, which converts ATP into cAMP. Then cAMP acts as a second messenger which activates portein kinase enzymes. The protein kinase enzyme converts glycogen into glucose.
This is a very complicated pathway for me. Why doesn't the cell just use adrenaline to activate the protein kinase enzyme? Or even more simply, why doesn't adrenaline itself be an enzyme? Doesn't this make things much more easier?
Or in other words, why does natural selection choose to use the more complicated second messenger as opposed to one messenger only?

If you think that second messenger systems are complicated, then do not look into signal transduction cascades. More complexity allows a finer regulation as well as signal amplification.

The question seems to assume an underlying idea: that adrenaline has nothing to do other than cause the conversion of glycogen into glucose.  It has many other functions; if you consider that, perhaps you'll understand why this multi-stage system evolved.

Does this answer your question? Apparent paradox in Glucagon action. It is obviously not the exact same question, but careful reading of my answer will help you understand how the integration of different biochemical responses between tissues is key to hormones and second messenger systems.

A simple explanation for why there are intermediate messengers between stimuli (in this case adrenaline) and the final effector (the kinase).

Multiple messengers in a signalling pathway create different points at which signals can converge or diverge: Many stimuli may have the same end result, so a common secondary messenger is a point in the pathway for these signals to converge, as opposed to having multiple dedicated proteins to produce the same result for each stimulus. cAMP is a good example of such a secondary messenger where the signals from many stimuli can converge. Similarly, secondary messengers can also be points where signals diverge to have very different results, depending on other factors/proteins that may be active in the cell at the time. This way, a cell has common points to combine information from multiple stimuli (which may be be in agreement or conflicting) into an output. If there was a strict 1-1 relationship between stimuli and effectors with no cross-over points, it would be difficult for such cross-talk to happen.

Signal amplification: Many times, cells receive only a few molecules of a stimulus, which may not be enough to trigger a response on its own. However, if there are intermediate steps in the signalling pathway where the signal can be amplified, then very feeble external signals can also be detected. This image illustrates this point:

Image source

There is already an explanation of amplification here which gives the detail needed for a naive student to understand.

The figure is also unintelligible on its own. What is D? I know what a GPCR is, but someone new to the subject would not. Please avoid using abbreviations without defining them.


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mRNA vaccines: Can a spike protein by itself have different side-effects than the virus itself?
I was wondering, is it possible for the isolated spike protein, as resulting from an mRNA vaccine, to cause harmful side effects in an individual, that would not have developed in that individual if it had been exposed to the actual virus? I am wondering about the spike protein in particular, i.e. I am specifically excluding any other compounds contained in a vaccine, but I would include "side-effects" caused by the spike protein of the actual virus.
The only way I could imagine this to be the case, if by being isolated and this being quite a lot smaller compared to a whole virus, the protein could find its way into areas of the body where it could "fit" otherwise.
Am I correct in assuming that the side effects that had been observed so far for these vaccines could be explained by an individuals immune reaction, rather than the spike protein itself?

In both infection by the virus and mRNA-mediated expression of the spike protein, spike proteins are produced in the host cell as membrane-bound proteins; they're not just separate particles floating around. Whether or not the rest of the viral machinery is present, these will end up displayed in the membrane of the infected cells. Here's a diagram showing that process in infection (note the little "blue spikes" in the cell membrane at the far right):

Figure from Duan, L., Zheng, Q., Zhang, H., Niu, Y., Lou, Y., & Wang, H. (2020). The SARS-CoV-2 spike glycoprotein biosynthesis, structure, function, and antigenicity: Implications for the design of spike-based vaccine immunogens. Frontiers in immunology, 11, 2593.
B-cells will recognize these foreign antigens, again whether their production was initiated by the virus or by a vaccine (here the equivalent of the "blue spikes" in the first figure are the "green S protein"):

Figure from Teijaro, J. R., & Farber, D. L. (2021). COVID-19 vaccines: modes of immune activation and future challenges. Nature Reviews Immunology, 21(4), 195-197.
(note: don't be fooled by the separate mRNA and AdV vaccine strategies here; the outcomes and mechanisms are the same, the diagram is just condensed to show both in one figure)
With mRNA vaccines, production of spike proteins is limited in time and space: to the cells that take up the injected mRNA, and only until that mRNA is degraded.
With normal infection, production of spike proteins is only limited by the course of the infection: as long as the virus continues to replicate, spike proteins will be produced in the membranes of affected cells, and can be produced anywhere in the body that the virus spreads (though principally in the respiratory compartments where the virus preferentially infects).


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What is causing these lichen patterns on a tree in Scotland?
I recently saw these lichens growing on a tree in Scotland. What is causing the pattern of dark lines? Are these the boundaries between individual lichens? Or could it be something to do with the growth of the tree (which is of diameter around 15cm)?
I'm more familiar with lichens growing on rocks, where these spatial patterns can potentially be used to improve rock dating (see e.g. this article). Presumably lichens growing on tree bark are younger, but are potentially affected by other factors that don't apply on rock e.g. changes in the bark as the tree grows.


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Are there any natural forms of aquatic vegetation which do not stand up in water?
We are carrying out some experiments where we study influence of underwater vegetation on waves. Unfortunately, the stalks of artificial 'vegetation' which we have seem to be too dense (or too stiff). The stalks sort of stand up a bit when you put them in water but they do not stand upright and all stay partly bent over.
This might be OK depending on whether there are any natural forms of aquatic vegetation which are sort of 'bent over' due to their weight under the water and which do not 'stand upright'? Is there any natural vegetation which does this?

Can you post a picture of how they are bent over? - many aquatic plants such as lagarosiphon will bend over near the surface. Are you thinking fresh or salt water?

Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.

Welcome to Biology.SE. Please clarify and focus your question. In particular, your title and body seem to be requesting the different information. Do you want examples of aquatic plants that are highly flexible or are you asking for plants that behave similarly to your artificial model. In either case specifying the type of environment (eg.s: marine vs. fresh, tropical vs. temperate vs. polar) ——— To me it seems like you should start with a survey of what plant(s) are most relevant to your research and then characterize their behavior rather than trying to find plants that fit your model.

If by aquatic vegetation you mean things that grow in deep water (as oppose to shore or marsh plants), I think pretty much all of them do, unless they grow as a carpet on rocks &c.  Consider kelp as a stereotypical example: why should it develop stiff stalks (which might break in strong waves) when flexible stalks and air bladders work better?  If you want something artifical to mimic typical seaweeds, try water ski rope.  (The kind that floats - polypropylene?)

double posted here https://pets.stackexchange.com/questions/32859/are-there-any-natural-forms-of-aquatic-vegetation-which-do-not-stand-up-in-water

@jamesqf do you know of any papers where the water ski rope is used to mimic floating seaweeds?  Are there particular types of seaweed which are well-modelled by this rope?

@Tom: No, pretty much all I know of seaweed and water ski rope comes from scuba diving and water skiing :-)

Yes there are many aquatic plant species which do not stand up in water.
You need to look at the lifeform of the plants, such as introduced by Raunkiaer ( https://en.wikipedia.org/wiki/Raunki%C3%A6r_plant_life-form ) and later work by Ellenberg & Mueller-Dombois (1967).
In fact, you're mixing up two different lifeforms :

true aquatic plants are unable to "stand up" : they are waterborne so they "bend over" depending of the water currents. You'll find rooted aquatic plants as well as rootless ones which float free above or within the water column.

European examples of rooted true aquatic (freshwater) plants are in the families NYMPHAEACEAE, CERATOPHYLLACEAE, HALORAGACEAE, RUPPIACEAE, ZOSTERACEAE, POTAMOGETONACEAE, ZANNICHELLIACEAE, CALLITRICHACEAE, NAJADACEAE and  RANUNCULACEAE (Ranunculus subgen. Batrachium)

helophytes is the name of plants which stand in water (usually have their roots and the basis of their stalk within water) but are erected and have aerial part standing up outside the water

European examples of helophytes are : Sparganium, Typha, ALISMATACEAE, many JUNCACEAE and CYPERACEAE, some POAECEAE (Phragmites, Glyceria, and a long etc.), and many other plants in many families.
For european France, Philippe Julve gives a comprehensive list of all plant species with mention of their life form, so you can look up species which correspond lifeform of your interest. Look here for the "CATMINAT" folder and then baseflor.xlsx and look in the first tab the column R "Type_biologique" (which means life form).
You will want to look the meanings of the abbreviations in the "Légende" tab of the sheet, column G. Julve consider true water plants as a sub-category of other main life form, so you'll want to search for "something-aqua".
Since you're interested in aquatic vegetation, you may want to look at some phytosociological catalogue like E-VEG (on the left side you can browse the tree to section "1 Marine waters" and "3 Freshwater aquatic vegetation".
Clic on one sub-category (latin names of vegetation units) will open the corresponding record in the main frame where you'll find indication to some litterature. But it may be of more interest for you to browse some academic catalogue for the latin name of the higher vegetation units + name of your area of interest. For instance you may want to look for Stuckenietea pectinati + Europe.
Be aware that E-VEG choose to follow botanical nomenclature (so when the main species after which the vegetation unit is named change its name, then the vegetation unit's name change as well, so when Potamogeton pectinatus became Stuckenia pectinata then the Potamogetonetea pectinati became the Stuckenietea pectinati). But many other phytosociological catalogues choosed to conserve the vegetation unit's names stable regardless of plant name's changes. So you may prefer to look for Potamogetonetea pectinati + South-East Asia (if that's your area of interest).
If E-VEG don't suit your needs, you may want to take a look at other catalogues referenced here.


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In a skeletal muscle contraction, what happens after ACh binds to the nicotinic iontropic receptors on sarcolemma?
Does the bound ACh becomes unbound and then gets hydrolysed by acetylcholinerase?

Acetyl choline, which is released at the neuromuscular junction is continuously broken down by the enzyme acetylcholineesterase into acetate and choline. Choline is once again taken up by the neuron through choline carriers to regenerate acetylcholine. This process continues as long as an the neuron is stimulated.
Source:
Wikepedia

That's correct, acetylcholineesterase is a hydrolase (An enzyme which hydrolyzes choline esters (Such as Acetylcholine).


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What happen if we inject restriction enzyme into the blood
Just a curious question, if we extract restriction enzyme and inject it to our body, what happen?

Does antibody recognize and block it?
Can restriction enzyme pass over cell membrane and destroy the DNA of a living cell ?

The appearance of any foreign antigens (e.g., proteins like restriction enzymes fall n this category) in the circulatory system should trigger an immune response.
There are actually two membrane barriers that the enzymes have to traverse to gain access to the nuclear genome: the cell membrane, and the nuclear membrane.  Proteins are typically too large and too charged to cross a lipid bilayer membrane--unless there is a pore (like on the nuclear membrane) or receptor for the protein on the cell surface.
When cells are engineered to express foreign restriction enzymes using transgenes, then yes, if the protein can enter the nucleus then the enzyme will start to digest all of its recognition sites.
Jasper Rine demonstrated this for the Baker's Yeast S. cerevisiae in 1986.


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How important is non-binding site of protein?
Just a curious question:

What will happen if i remove most protein sequence that encoded for non-binding site of Restriction Enzyme to make a new enzyme, can the new restriction enzyme still work?

No. The rest of the protein contains catalytic and structural domains that are essential for its proper function. Some domains may be redundant, but you can't willy-nilly chop everthing off and still expect one part to work.

As it seems with about everything in protein science, the answer is it depends on the protein.  Many proteins will lose activity if they are truncated; however, I've worked with GPCR's that were truncated down to the extracellular portion only and they showed consistent kinetic results.  Antibodies have been cut into pretty tiny chunks (scFv's) to create some drugs like Pexelizumab. Some proteins can be hacked down quite a bit, some can't be at all.

The active site usually consists of amino acids from multiple different regions of the enzyme. So if you remove or replace parts of the protein chain then the structure (folding) of the enzyme will be most probably different and the active site will cease to exist. On the other hand in lucky cases replacing a few amino acids can increase the catalytic activity.


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Can we create custom gene/protein?
Does it possible to create any custom gene or protein we want with current technology?
I have a protein sequence or a gene sequence about 4000 bp write down on my computer, is there anyway to "print" it to real gene molecule or protein molecule (for example use chemistry and enzyme and automatic machine..) ? What is the challenge ?

Yes, this is possible. The challenges depend on many factors that are specific to the gene/protein. I don't think this can be answered in a generic way.

Yes, there are well established methods for synthesizing DNA with any sequence you want. Several commercial companies will accept DNA sequence (a text file) and generate the DNA for you. Genscript for example is well known.
Synthesizing the protein can be bit more tricky, depending on what it looks like and what you want it for --- proteins are way more heterogenous than DNA. There are commercially available cell-free protein synthesis systems that might be useful if you are merely interested in a peptide. Most people express the protein of interest in cultured cells though. In either case there is some biochemistry work to purify the produced protein. Genscript provides protein synthesis services as well. (No, I'm not paid by them, just don't have the energy to google other companies :)
In most cases, this works fine, and with a bit of tweaking you can produce quite large amounts. But for some proteins that depend on posttranslational modification for their function, expression can be difficult: see Can any enzyme be produced?


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Do transposons usually jump from one chromosome to another?
If it is usual occurrence, does it mean that my one gene can change its location from one chromosome to another?

Yes of course; they are not like tandem duplications.
However, some transposons have site preferences; for example the Tn7 transposon.

EDIT:
I don't know what you mean by original location. Some transposons, especially LINEs, have expanded a lot in the human genome. For any individual you can check the germ cells for a reliable estimate on the original positions. There are mechanisms such as piRNA mediated silencing that suppress transposon activity in germ cells. The genome of the germ cells also tells you what exactly will be inherited by the offsprings.

An old thread, but I have a similar question: can you (or anyone else) provide an example of a transposon that moves from one chromosome to another chromosome?

Transposons are specialized sequences of DNA that are part of a larger group termed mobile genetic elements. They can move from one position in the genome to another on the same chromosome or another. A specific enzyme called transposase, usually encoded by the transposon itself, acts on specific DNA sequences at each end of the transposon, causing it to insert into a new target DNA site (Alberts et al, 2015). Not only is this a source of genetic variation, genes carried in this way can convey great advantages such as carrying antibiotic resistance in bacterial cells.


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Are dominance hierarchies always maintained through violence?
Is there a species in which a dominance contest cannot escalate to a fight? I don't know of any but I'm not a biologist.

I too cannot think of any such species. I think dominance is simply based on "if you are a better alpha male, then defeat me" rather than "if you are a better alpha male, then be more patient than me" ;)


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Why Do we close our eyes while sneezing?
Google says germs  may fall on eyes from our sneeze but it happens all the time . Also it says it a part of contraction. What may happen if we sneezing wirh our eyes open ?

When I sneeze i keep my eyes open esp when driving.

Mythbusters did this one!
The simplest response is that your eyes close as a reflex, because the nose and eyes are linked by cranial nerves which brings the sneeze signal to the brain and then to the eyes, making them blink. Would you eyes pop out if you managed to sneeze with them open? (a common urban myth) No! Your eyes are attached by strong muscles and it would take a lot more force than a simple sneeze to lose them.
Mythbusters article on the subject
I would love to give you a more scholarly article but this is the same one referenced on wikipedia on the subject, plus it's hard to find academia in the fluffiness of this question.


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What is the name of this flower?

This is from Bangladesh though I am not sure it's native here

Google image search gave me answer as "Plumeria"

I never knew that was possible with Google Images. +1 :D

Google has lot of such very less known functions :P

White Frangipani: Plumeria Spp. In Bengali: কাঠ গোলাপ (pronounced Kath Golap). Straight translation is wood rose or pink and they do have rose color.

Also known as FrangiPani in Africa. Has lovely sweet scent, I have a white and pink tree in my garden, they are about 8 ft tall. Doesn't like frost


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What exactly is bound by the control line on COVID19 antigen tests?
Clearly the test line binds some component of the coronavirus, I believe most commonly the nucleocapsid protein (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8049777/). However, despite extensive googling (and Google is doing a lousy job of understanding my question) I have not been able to figure out what is being bound by the control line. Probably it differs by test manufacturer, but I'm sure there are some relatively common antibodies that are used in the control line?
My best guess is that it should test for some common mucin or collagen or elastin but this is based on nothing.
The reason I'm asking is that I want to understand if the "control" line being present is a good indicator of the test having been done properly. Let's say some person:

rubs the swab on a different body part than the nasal mucosa
or doesn't touch the body at all with it
or swabs the nasal mucosa very briefly
or only inserts the swab into the buffer solution extremely briefly

would the control line still show up?
I'm not simply trying this myself at home because it's annoying and expensive to get lots of tests simply to waste them to test their limits.

Related: https://biology.stackexchange.com/questions/101767/whats-happening-in-the-c-and-t-stripes-of-a-covid-test-kit/101777#101777

According to biotrend (SARS-CoV-2 (Covid-19): Rapid Antigen Test for Diagnosis), the control line has an immobilised Goat anti-chicken antibody. There, a chicken-IgY gets stuck which was carried from a conjugate pad by the sample fluid.
So even pure buffer solution would yield a positive signal at the control line. It seems that the control only tests for proper reactivity of the antibodies contained in the conjugate pad, and not for proper usage by the user:

A colored band in the control region serves as a procedural control, indicating that the appropriate sample volume has been added and the membrane is functioning.

This manual (health.govt.nz) reports that whole blood and Mucin do not interfere with the test (including control?). It sounds as if biological fluids are meant to be ignored by the test in general.

Indeed, this is why the control line is so stupidly designed. It should check not only for proper functioning of the test but also that the user did not just put pure buffer solution! Otherwise a negative test is not convincing even if supervised.

@user21820 No, this is not stupid because you need a control that shows that your test is valid which is independent of the sample. Having a positive control would sometimes be nice but makes the interpretation more complicated. Not to speak of the need to have a control that under no circumstances will produce a false positive result.

@Chris: You claim "you need". I disagree. What we need from the test is a way to distinguish between covid infected and non-infected. The way the tests have been designed is inferior for that purpose. For what I suggested, there is no complicated interpretation at all. (1) No control line ⇒ Test invalid. (2) Control line ∧ Test line ⇒ Infected. (3) Control line ∧ No test line ⇒ Likely uninfected.

@user21820: yes, in theory that sounds good. However, using a user dependent positive control introduces another variable, where the test may fail (making the test look worse compared to others). Also, it wouldn‘t ensure proper usage, since it does not prevent a user from applying an older/someone else‘s healthy sample. Supervision or Conduction by professionals is the only solution. I think it‘s smart.

@user21820 Believe me, you need this. What do you do with tests where the positive control is absent but the test band is present? Also: How do you control if the test is working at all? Antibodies are stable, but still storing conditions are important to ensure a result.

@user253751 - I know, I‘ve been there, like everyone else. My point was that a user dependent positive control doesn‘t prevent fraud, hence it‘s worth can be debated. (For me I‘d feel more comfortable with sth like a Mucin control, but it‘s really not that necessary, given that these tests are expensive enough)

@Chris: What user253751 said... No control line ∧ Test line ⇒ Probably infected but you should get another test done because you botched the first one. If you keep botching tests unlike everyone else, then go to a hospital or clinic.

@markur: This isn't just about malicious testing. Even an honest person can't be sure that they have swabbed enough if the control line doesn't give them any feedback.

@user253751: Test line appearing but no control line does not mean you have COVID. It means something went wrong that caused colloid to deposit at the test stripe, but not at the control stripe. You can say in that situation that the test is unreliable, but not more. The control is meant to guard against false negatives due to errors in the manufacturing process or due to storage conditions.

@user21820: sure "non-contact swabbing" will cause false negatives. But: even proper swabbing (taking up sufficient mucin) is subject to sampling error due to spatial heterogeneity. And there is indication that this is a substantial source of error (I've seen some very early paper in 2020 looking at a series of PCR results from  back-of-the-throat swabs of the same individual, and roughly a quarter of those was negative. The rapid test sampling procedures like nasal swab are considered to have sufficient sensitivity in practice compared to that standard. The question is: compared to that, ...

... would an additional mucin control line be worth while? In particular, since a doubt about sufficient swabbing (e.g. by someone overseeing the test) can be resolved by doing another test (from the same lot). But a manufacturing or storage problem is likely to affect all kits of the lot or the boxes at hand.

@cbeleitesunhappywithSX: I didn't say you must have covid. That's why I used the word "probably". The likelihood of a manufacturing error is much lower (<0.1%) than the likelihood that the test line shows up positive but the person does not have covid. Yes, an entire batch may be faulty, and that's why I said "should get another test done".

@user21820: no, that was user253751, to whom also my comment went. Still, you're not doing the comparison we need here. In particular, we'd need the (posterior) probability of the SAR S-CoV2 line of the test being correctly positive given that the control line did not show up. Your < 0.1 % for manufacturing error is only the the prior (BTW do you happen to have a reference on this - this is not to raise doubt on the number in case it's a guesstimate, it's that I'm professionally interested in any such ref), but the data (control not showing up) is actually very strong evidence here...

(prior of manufacturing/storage error: I didn't see that many test kits, all in all ≈100, but there were some in there which were obviously short on extraction buffer). For the practice of covid testing, the 2 € for a test kit makes the discussion moot, since the practical answer will always be throw it away and do another one. But we're on biology.sx here where other lab tests are discussed as well, and I'm analytical chemist: it is an important point to me that an invalid test is invalid and it is wrong to use it for anything else than possibly digging into fault modes.

@DanielHatton these are most likely to be recombinant anti-species antibodies, as their performance is much more similar lot-to-lot than animal-derived polyclonal antibodies.

@cbeleitesunhappywithSX: There's clearly a difference in our goals. In my view, the purpose of using the ART is not to get a near-zero false-positive rate, nor to get reliable statistics of covid infection. Rather, it is to provide confidence that you do not have covid based on the ART result! If you have that goal in mind, then you will understand why I say that my suggested version is better, and why we do not need the conditional probability of infection given no control line but a positive test line.

If you follow my stated procedure (including getting another test done if the first one has a problem), then that probability is irrelevant. Rather, it is the probability of manufacturing error that is relevant, because that would give an upper bound on how likely there is a problem with the ART in the first place. You can't just treat this ART testing as a lab test. It is not, because its primary purpose is as a tool for dealing with the pandemic. Whenever I use the ART, I want to know ( likelihood of covid given negative ART result ), not ( likelihood of no covid given positive ART result )!

@DanielHatton yes, they're all recombinant. However, recombinant doesn't necessarily mean monoclonal - the final product could be a mix of two or more different clones to give the desired characteristics to the batch. I used to work at an antibody company that did this.


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Why are newly grown leaves red?
After a period of heavy rain, several trees in my garden will put out an impressive burst of new leaves, with an incredible vibrant red colour, almost the colour of port wine. The new leaves will then slowly turn green.
I understand that the leaves turn green once they start producing chloroplasts and chlorophyll, but what is responsible for this initial red colour that is so very vibrant? And what biological role does it play?


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Why can't we use plasmids to add genes to ourselves?
Reading these answers I wonder, why doesn't "gene therapy" use self-contained plasmids instead of trying to splice a length into a chromosome?

IIRC humans have several mechanisms that digest extra-nuclear DNA. Unfortunately I don't have a reference handy, but I'm 95% sure any plasmid would just be destroyed.

That makes sense.  So "some yeasts" is the exception, having first evolved a mechanism to allow importing of survival traits, possibly trading off resistance to viruses.

In mammalian cells, Plasmids are not replicated, which is why in cell culture, you need the extra step of recombining the vector into the genome via homologous recombination. The issue is that this can be done in vitro to cells, but once you try doing it on an organism level there are many problems. One is that Adenovirus usually needs to be used to insert the vector. But adenovirus' capsid can only accommodate about 10kb of DNA. As most homology arms are at least 10kb, each, you cannot do targeted integration. You would need to rely on random integration, and you couldn't predict the effects.

First, plasmids do not usually integrate into the chromosomes of human cells. In the laboratory, plasmids can be introduced into the cytosol of cells, and plasmid DNA will then be "read" by the host cell and used to make new proteins, for example. But plasmids usually remain separate from the cell's own DNA, and in that sense they are not effective for gene therapy.
Second, our cells are quite good at detecting and destroying plasmids, as well as other foreign DNA. This is a self-defense mechanism, evolved to get rid of viruses and other nasty parasites that might be trying to hijack the cell. In the lab, where we are working with isolated cells in a culture dish, with no immune system, plasmids are typically tolerated. But in a human being, immune cells that have specialized in detecting intruders are very competent at detecting such manipulations, and they will quickly sound the alarm and wreak havoc ... So if injected into the body, plasmids are quickly detected and destroyed.
Research in gene therapy aims to find more efficient ways of "editing" the DNA of human cells, ultimately in a way that can be safely applied in the body. Such a technique does not exist yet. The latest CRISPR-Cas9 gene editing system is a phenomenal tool, and is very efficient at getting into the DNA of human cells; but the CRISPR-Cas9 proteins must themselves be delivered into the cell, for which a virus is typically needed, and this would again cause immune reactions if attempted in a human body.

I believe we could use plasmid insertion to assist with gene therapy. EBV can maintain a plasmid in the cells it infects and the plasmids can effectively replicate. With a greater understanding of the latency and the implications of inserting genes using EBV, it may be possible for gene therapy to occur via genes on a plasmid.
references: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2562867/
http://jvi.asm.org/content/65/1/483.full.pdf

Can you elaborate on «EBV can maintain a plasmid in the cells it infects» in light of Roland’s answer that they are seen as invadors?

This is a very interesting answer. Whether or not it has any relevence to gene therapy, it  is valuable as background information that most people will not be aware of. It could be improved further by better layout and some elaboration. I would split it into three paragraphs: 1. Explain what EBV plasmids are, stressing the eukaryotic replication origin as opposed to the bacterial one the poster may have been thinking of,  2. Suggest how they might be used for gene therapy, 3. list the references.


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white and brown mushrooms. same species but...?
On Cooking SE and Wikipedia we wonder if someone can claify:
Are white vs brown immature fruiting bodies of Agaricus bisporus different stages of development like many kinds of fruit change color as they ripen? Or are they different cultivars or are they due to different environmental conditions when forming?
Bonus: what isnthe brown pigmentation? Is the difference in taste due to that or meerly correlated with it but due to some other difference?


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What genes are required to make E. coli photosynthetic?
"All" of the genes for bacterial photosynthesis were discovered in a gene cluster almost 40 years ago. Marrs, J.Bact.  What more is needed to make E. coli photosynthetic?

Related post https://biology.stackexchange.com/q/17676/3340

I think the crux of the answer is only hinted at in WYSIWYG's answer. The crux of photosynthesis is partitioning coupled reactions.

Photosynthesizing plant cells have sub-cellular structures called chloroplasts; their membranes are especially important for the compartmentalization of different functions and chemical processes for the entirety of photosynthesis to even be possible. Partitioning is difficult to achieve in E. coli, and that to me seems a necessity for achieving true heterologous, truly ectopic photosynthesis... Even photosynthesizing cyanobacteria (photosynthesizing prokaryotes) possess thylakoids, membrane-bound compartments where the magic happens. Photosynthesis though can certainly proceed and be made more efficient in single cells (example).
That leaves us with a simple answer: engineering E. coli with thylakoid-like structures is not really practicable. Why not simple use cyanobacteria instead?
Further reading: review on single cell photosynthesis in single cells.

A very basic kind of photosynthesis can be realized in E.coli by expressing a rhodopsin (Kim et al., 2017). Rhodopsins are membrane proteins that can pump ions (including protons) across the membrane and generate a transmembrane potential. When coupled to ATP synthase, rhodopsins can cause ATP generation in the presence of light. In an earlier work, Hara et al., (2013) had expressed a rhodopsin in mammalian mitichondria to make them synthesize ATP in response to light exposure.
This is not the kind of energy efficient photosynthesis that we see in cyanobacteria and plants. The group of Ron Milo have engineered Calvin-Benson cycle (carbon fixation) in E.coli, and optimized carbon fixation using adaptive laboratory evolution (Antonovsky et al., 2017; Gleizer et al., 2019).
Engineering the entire photosystem in E.coli would be a difficult task because a functional photosystem does not merely involve expression of the pigments but also their 3D assembly into functional sub-cellular "organelle" like structures.

Has either a simple anoxygenic reaction center or bacteriorhodopsin been expressed in E. coli in a functional manner so that the organism can energize its membrane via light?

@Youvan Check out the first reference. It also cites previous work on this topic as well.


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Traceability of a mature tree to its original seed via DNA
Is it possible to trace a specific seed to a fully mature tree?  For example, Can a seed be traced to the full-grown plant based on DNA?  Would it be possible for me to catalog a seed DNA and then years later be able to identify the full-grown plant to that seed that was cataloged?

I'd think it would be difficult to obtain the seed DNA without killing the seed.

Apart from the difficulty pointed out by @mgkrebbs, this is no different from the use of the DNA in forensic science... of course, if we are sure that the seed contains only one type of DNA.

@mgkrebbs — That really depends on the size of the seed — I worked in a maize lab and we regularly removed a small portion of the scutellum for genetic or other analyses (this can however impair seed viability). So, this could be done easily for trees with a large seed (e.g. nuts), but would be much more challenging for the many trees with tiny seeds. WesleyRios — you would need to determine viability over time after sampling to make this work.

As the embryo of a seed typically contains many cells, it should in theory be possible to obtain DNA from a seed without disrupting it (there may be pragmatic issues with protocol, depending on the particulars of the seed).
If you have the DNA and each seed has been produced by a separate fertilization event, then each seeds DNA would be unique and it should certainly be possible to identify an individual genetically, just like it is with animals.
Not all seeds are genetically distinct however. For example, many plants will also produce seeds asexually under appropriate conditions, a process known as apomixis. If the seeds are being produced asexually, then your only hope would be to identify different mutations in different seeds, which is a much fainter signal and likely to fail for your intended purpose.

Thanks for the response.  When you say "separate fertilization event", what do you exactly mean by it pragmatically speaking?   For example, if I have a tree that produces the seed during a specific time of the year, would that mean that the seeds for that season are part of the same fertilization event?  Hence, the DNA for all the seeds would be the same?    I appreciate the education.  Thanks again

Plant reproduce sexually by combining gametes, just like we do. In the case of a plant, the male gamete is pollen and the female gamete is called the ovule, which is analogous to an egg. So during sexual reproduction, your typical tree gets "pregnant" with massive amounts of "fraternal twin" seeds, each produced by a different grain of pollen meeting a different ovule.

@jakebeal: It also seems possible (theoretically: I don't know whether it really happens) that one pollen+ovule fertilization could produce many seeds.  E.g. in many plants we see individual seed capsules containing many seeds in a regular pattern.  If each one required a separate pollen grain, you'd expect randomness, no?

@jamesqf Surprisingly, no! For plants with seeds in a regular pattern, the ovules generally develop in a regular pattern, each putting up its own receptor for pollen (though these are often bundled together also). Corn is a particularly good example: each thread of corn silk leads to a separate ovule, which will be separately pollinated and become a separate kernel. It's biology, so there are probably exceptions, but in general it seems that flowering plants pollinate their seeds separately.

@WesleyRios, the implications of the above is that most every tree seed will be genetically unique.  You cannot tell from the offspring-tree's DNA what time of year its seed was produced, nor what year.  With significant effort in advance, you might be able to determine which two trees were the parent trees if you collect the DNA of each of the potential parent trees (which usually would be large number) before they die.


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What does this mean?
The phenotypic ratio of dihybrid cross 9:3:3:1 can be derived as a combination series 3 yellow: 1 green, with 3 round :1 wrinkled. This derivation can be writtenbas follows:

(3 round :1 wrinkled) (3 yellow: 1green)= 9 round,yellow: 3wrinkled, yellow: 3 round,green: 1 wrinkled, green

I only understand the phenotypic ratio but what is the above series mean?

The characteristic(or trait) which is visible in an organism is called its phenotype. The ratio of the phenotypes of the progeny produced in a cross of trait(s) gives us the phenotypic ratio.
A dihybrid cross refers to a cross in which plants having two contrasting characters are crossed with each other. For example, crossing round and yellow seeds with wrinkled and green seeds is an example of a dihybrid cross where the contrasting characters are as follows:
1. Round and wrinkled seeds (contrasting on the basis of the seed shape)
2. Yellow and green seeds(contrasting on the basis of seed color)

The above image gives us the perfect example of a dihybrid cross where two heterozygous parents (RrYy and RrYy) crossed with each other to form four new progenies:

Round and yellow (RRYY or RrYy or RRYy or RrYY)
Round and green (RRyy or Rryy)
Wrinkled and yellow (rrYy or rrYY)
Wrinkled and green (rryy)

We will observe that for instance if 16 progenies are produced, then 9 will be round and yellow, 3 will round and green, 3 will be wrinkled and yellow and only one will be wrinkled and green.
This brings us to the conclusion that the phenotypic ratio of a dihybrid cross is always 9:3:3:1 regardless of the number of plants progenies produced. For instance if there are 60 progenies produced then :

Number of round and yellow seeds will be - 9/16 of 60
Number of round and green seeds will be - 3/16 of 60
Number of wrinkled and yellow seeds will be - 3/16 of 60
Number of wrinkled and green seeds will be - 1/16 of 60

You can reach this site for further clarification

Great answer. It is important to mention that 9:3:3:1 are the odds of each phenotype occurring and not the actual fraction. We have statistical tests (like chi-squared) to see if a population is behaving in a mendelian form.


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What happens if a population of songbirds increases rapidly without predators?
Suppose there’s an area where there’s a rapid increase in the population of songbirds and no presence of predators.  What type of detrimental effects, if any, would this have on the environment in that area?
I’m guessing at least a reduced insect population but I’m not sure about some of the other effects such as plant life or generally how songbirds function in the predator-pray cycle with respect to any particular environments.

Welcome to Biology.SE. Please take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. In particular, your question is 1) unfocused and 2) shows no evidence of prior research. 1) You are asking for a textbook, which is not reasonable (answer will vary with both habitat and bird species). 2) You haven't said where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Both of these are considered to be reasons for down-voting and closure on this site.

I’m voting to close this question because it is much too broad and under researched.

Likely result in an increase in Cooper and Sharp Shin, and possibly other hawks(US). We had hundreds of Goldfinches, Pine Siskins and others at our bird feeders, then Cooper hawks moved in and we see only a small fraction of the number of birds previously here. Most of common song birds eat seeds, not insects. Robins being a notable exception, eating worms and fruit. Warblers are insect eaters but seem to stay rather dispersed and most people would not hear their songs. I have never seen any detrimental environmental affect of song birds; the American Beauty berries, wild grapes, etc slowly disappear over winter. But other than an occasional flock of Cedar Wax Wings, it is not apparent that birds are eating them.