text:
Is it possible to become pregnant indirectly?
Is it possible to become pregnant indirectly? For instance, if there is some wet semen left behind inside tight clothing, jeans for example, and a woman tries them on for a couple of minutes? What is sperm's motility after it's deposited on cloth in room temperature? Can sperm still swim inside from outside if it's near the vaginal opening in the cloth? What are the chances of pregnancy if the woman is/is not wearing any underwear?

Good question but poorly narrated. Refine your question by reducing questions to just single one. It's sounding pretty curious but snappy question. Once refined, it will be very good question

yes this is possible, as long as the sperm make it onto the mucus membrane of the vagina. the LIKELYHOOD depends on the fabric and how much semen is in the fabric, if it's still clotted or not, and environmental factors.

Sorry, I forgot to add that I meant liquefied semen on the cloth so that it appears as a wet spot, the kind of semen smudge you get when it has seeped through thin clothing (underwear) before being deposited on that outer layer (jeans).

if youre being that specific, it probably happened to you. take a pregnancy test. if positive, there is sadly not much you can do except murder the unborn child. his body your choice


text:
Identify this insect, found in Central Vietnam, with long antennae, black wings, and red body
Last year this insect landed on my hand when visiting the My Son city ruins in Central Vietnam.
I've been trying to identify the insect, but until now without result.
Can you help me? Or do you know who could?

That is a pretty cool bug.

Upvoted for the nice photo!

This is a male scale insect, which are Hemipterans from the superfamily Coccoidea.
The one in your photo is probably from the Genus Drosicha. Here is the Wikipedia page for Drosicha corpulenta.
Here is an image, for comparison:

Here is another one, with black antennae, like yours:

There is no doubt that your specimen is a male because sexual dimorphism in Coccoidea is huge. Have a look at the females of Drosicha:

In conclusion, determining the exact species here is very difficult. However, we can be sure that the Genus of your insect is Drosicha.

This question has been asked before. It's Identify this insect, found in Central Vietnam, with long antennae, black wings, and red body
And it is Drosicha corpulenta. I'm having trouble finding a credible source.
Try these: google[http://nc.biodiv.tw/bbs/showpost.php?p=19392&postcount=1]
google[https://isabellevea.wordpress.com/2014/05/27/the-giant-scale-drosicha-corpulenta-on-uncovering-its-biology-part-1/]

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sort: votes


text:
Species I.D. hardwood tree
There are two of these trees, growing in old fence rows, along my yard, in central VA, Augusta County, Shenandoah Valley.  They have smooth, leathery leaves, pale wood, quite hard to cut, and tough to break.  The close ups are of some limbs I trimmed, yesterday. The biggest is about 10 inches in diameter, and perhaps 40 feet tall.  Branches tend to grow strangely hooked elbows that send branches off into strange directions, which makes trimmed limbs tangle and hook together.  This is what the foliage looks like in mid September.

Have you tried to split it? If you have, and it mangles instead of splits, it's a kind of a gum tree. Gums are very hard wood, impossible to split, and the branches hang down and seem gnarly. It's the only type of tree I know of that looks like that with those smooth, shiny leaves. (I had black gums in my woods.) Not 100% so no an answer.

I'm thinking this is a Quercus imbricaria, which has the nickname of "shingle oak"; they're native to the eastern regions of the United States, which includes your state and county, exhibited immediately below.

Distribution
 Brown = absent; Dark green = present in state/Native; Light green = present in county/Native.
(source)
The leaves
The leaves are mostly linear in shape, with entire margins & a combination of pinnate and dichotomous venation. The overall color, size and sheen also seem to match quite well.

Overall tree
Surprisingly, I had a difficult time finding a decent image that showed a close up of the branching for this tree, so I decided to use an image of a Quercus laurifolia instead, which is of the same genus as the proposed species, and is also found in the eastern [but more southern parts of the] United States.

Your leaf photos look very much like this tree.  An oak without lobed leaves hadn't occurred to me, and did not come up on tree identification apps I tried.  The trunk bark also looks very like oak. Thank you.

I turned up laurel oak while googling around.  But wouldn't the acorns give away it was an oak?  jpopelish - did you ever notice acorns?  An oak that size should make plenty.

I have not seen one acorn, in three years, from either of these trees.  That would have given away that they are oaks,  Both were badly crowded by sassafras and wild cherry trees, up until a year ago, if that is an explanation.

It generally take oaks decades before producing their first acorns, and is why I wasn't concerned too much with this during the IDing process. Also, once acorns are produced, future production is intermittent.

It is a Bay Laurel Laurus nobilis
If the leaves are brittle and crack when folded and they smell fragrant then almost certainly.
I would ask this first, but unable to comment until 50 reputation

Respectfully speaking, this is not the correct ID. The tree you propose have leaves that are ovate/elliptic/obtuse in shape, however, the OPs leaves are much more linear. I also believe your proposed tree's leaves have sinuated margins, whereas the OPs leaf margins are entire.

bay laurel is a bushy tree which doesnt have a pronounced trunk below the leaves. i didnt see a bay laurel taller than 4-5 meters.

I think these leaves are flexible and leathery, rather than brittle, though quite smooth and glossy on the upper surface.

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text:
Yeast contamination with fungus patch
I am working on yeast mutant and I am observing their sporulation efficiency on agar plates. One of my plates got some dark green small fungus patches. I can't grow yeast again and dump this one with fungus because I am counting at a specific time interval to compare and it will take a lot of time to go through the entire process.
What should I do? Should I remove fungus from scalpel? And does this fungus going to affect the yeast growth?

Either you can cut out the fungus and get away with it, or the fungus will rapidly overgrow your plate regardless.  You might as well try to cut out the fungus.  If it overgrows your plate the experiment with that plate is done.
This is why you should have parallel plates for this sort of experiment.  There is a saying: don't put all of your eggs in one basket.  The reason is that if you sit on that basket all eggs are broken.  If you are counting on just one plate for your experiment and you sit on it, or it gets overgrown with fungus you must start over.
The other reason to have several parallel plates going is that you can average the spore count.  One plate might have more or less for some random reason, like fungus.  But if you have several and average them out you will reduce noise.


text:
Orange tipped plant found in Carden limestone plains of Ontario
What is species is this plant?
Found in the Carden limestone plains of Cameron Ranch (near Orillia, Ontario, Canada) on September 9th, 2017.
It is located in an old bog that seems to have sphagnum peat moss (to my untrained eye).

It's an odd angle, but I think the plant/flower is an Indian Paintbrush (Castilleja coccinea). It is found in Saskatchewan, Manitoba, Ontario, and Nova Scotia.

They're in Alberta, as well.


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RNA extraction from soil
I have been trying to extract RNA from soil without success. I have used commercial kits (The Plant DNeasy kit) because I did not want to buy a complete new kit (Soil) to do 5 extractions. Is there any "in-house" protocol that successfully extracts RNA from the soil? Or, is there any tip that would allow me to extract good soil RNA using the Plant DNeasy kit?
Thanks


text:
Is there a purpose for nucleated red blood cells in reptile, avian and fish blood?
I have read, and read, and read documents on this subject but still have no conclusions.
Everything I have read explains why mammals don't have a nucleus (to make more room for the haemoglobin and allow for more oxygen to bind as well as making it easier for the RBC to fit through capillaries) but the reports don't explain why birds, reptiles and fish may still have nucleus in a red blood cell.
Is there really any other function a nucleus has within a red blood cell apart from being the 'brain of the cell?
It's doing my head in, all I've gained from this research is the understanding that birds have a far more advanced respiratory system and their capillaries are bigger than mammals, this still doesn't explain the need for a nucleus, it's actually suggesting they don't need one!
Any enlightenment will be great,
Thanks.
http://onlinelibrary.wiley.com/doi/10.1002/iub.490/pdf

+1 vote. I was also wondering this last time though I never bothered to research

Does there have to be an explanation? I personally would doubt the fairy story about mammalian red cells making room for haemoglobin. Typical post hoc justification. They just evolved differently.

Many good points already made above. I'd only add enucleate red cells confer a solid evolutionary advantage for many mammals. Apex land predators, eg cheetahs, probably couldn't sprint if they had the lesser capacity of nucleated red cells. Also allows some animals to occupy higher altitude niches - eg mountain goats etc

Small point: Camelids have enucleated erythrocytes, albeit elliptical ones. See https://vetclinpathimages.com/2018/03/27/normal-camelid-erythrocytes/

It's difficult for vertebrates to aquire/evolve enucleated cells, that's why they are very rare previous to the mammalian adaptation. Salamanders have evolved enucleated cells. Research suggests that it may be due to a salamanders big genome and big cell nucleus, compared to the salamanders small body size.
Mammals may have acquired the trait because they evolved from small animals with miniaturized capillaries and blood cells and large genomes, and the advantage was kept afterwards. Large genomes inhibit flow and flex of nucleated blood cells.

The smallest bird genomes are found in the most miniturized clades of birds at 1 Gb. Mammals of a similar size can have carry 2-3 Gb of chromosomes.
Lizards have lower energy than mammals.
Fish are most active in highly oxygenated water, i.e. salmon, which allows them to be very energetic, water is a more efficient breathing medium than air, hence the small size of gills. fish and humans both contain 6-7 percent blood by volume.
Birds have smaller haemoglobin including the nucleus, and have a different kind of capillary size and structure with advantages and disadvantages, and lighter hollow bones with less marrow. Birds didn't radiate to new shapes as well as mammals did.
Enucleate cells are fairly rare in the plant and animal world, so they perhaps have a hidden expense. Maybe it's not just a factor of shedding the nucleus, and in fact there is a cost of adapting the primary circulation system's immunity against paramecia and pathogens without a nucleus. various viruses can take advantage of enucleate cells.
Perhaps that is the reason why birds did not evolve backwards into dinosaurs. some factor made their genome comparatively small. It could be the lack of enucleated bloodcells that forced them to shed genes as an alternative. Perhaps that's why they lost the dinosaur genes which held code for quadrupeds, arms, jaws, horns and teeth and the things that birds don't have.

Thanks for all your answers, it's pretty much summed up what I had in mind!

May I ask what are your resources for your answer please? It's helped me a lot!

Thanks Steph, I mostly use google scholar for specific references, some of it is difficult to research, skeletal shape advantages and immunity and physiological adaptions of enucleosis is less easy to find specifics on.

enucleation is just one of multiple solutions to the same problem, and each has their own costs.
When compared side by side bird blood carries the same amount hemoglobin as mammalian blood. birds maximize oxygen content my evolving smaller hemoglobin molecules, mammals evolved smaller hemoglobin carrying cells.
Each solution has its own cost, bird erythrocytes still have mitochondria which reduces oxidative stress on the cells while meaning each cell is larger and thus capillaries need to be larger. But oddly, even though bird blood cells age slower (accrue oxidative stress slower), birds have a higher turnover of blood cells. Since enucleation limits the speed at which mammalian blood cells can be produced they cannot replace blood cells faster even though they are wearing out faster.
Once a group starts evolving down one of these strategies and starts evolving means to counter or at least mitigate the costs there is no benefit and quite a high cost in switching to a different method, much like both groups respiratory system they get locked in evolutionarily.
Only in mammals and birds is the demand for oxygen high enough for the costs to be worth it. They need to maximize blood oxygen carrying capacity and take the benefit outweighs the costs. Other groups don't evolve these specializations because for them the cost is not worth the benefit there blood oxygen capacity is more than adequate. Its the same reason they don't evolve the advanced respiratory systems of mammals and birds.
https://journals.physiology.org/doi/abs/10.1152/ajpregu.00276.2020
https://pubmed.ncbi.nlm.nih.gov/2012765/#:~:text=Mammals%20had%20more%2C%20smaller%20erythrocytes,exothermic%20groups%20such%20as%20reptiles.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3686644/
https://www.hindawi.com/journals/sci/2011/139851/


text:
Identification: Creepy 'nope'
While walking back from our routine evening stroll through the hills, we stumbled upon some insect(?). It was the size of an index finger, and it appeared to have some sort of wings. While I tried to take pictures of it, it started turning towards me with it 'claws'.
Additional info:

Origin: Romania, in the hills
Date/time: 17 August 2017, 19:15, sunset
Warm sunny day, just started to cool down, 19 degrees celcius

My wife doesn't want to go outside anymore unless she knows what it is, and she won't allow me to go and pet it.

Related: What species of insect is this?

That's some kind of mole cricket (Gryllotalpidae).
According to this website there's only three species found so far in Romania:

Gryllotalpa gryllotalpa
Gryllotalpa stepposa
Gryllotalpa unispina

It's most likely you've encountered a specimen of the first species as it's the most common and widespread one in Europe, Gryllotalpa gryllotalpa:

Due to the context of the question it might be helpful to add whether they are aggressive, dangerous, poisonous etc. or mostly harmless

Thank you very much. Even though they are common here in Romania, apparently actually meeting one is not an everyday occurrence.

See also: https://en.wikipedia.org/wiki/Mole_cricket, the one shown here seems to stem from Australia, though (see https://en.wikipedia.org/wiki/Gryllotalpa_brachyptera), the one from the question looks more like Gryllotalpa orientalis

@TobiasKienzler It indeed looks like the orientalis, but what's it doing in Romania?

@PierreDuc Good question, it probably hitch-hiked

@TobiasKienzler Stop it. Next thing you will start writing cricket as krikkit.

@MrLister Oh no, I wouldn't do that. Not again.

To answer whether they are dangerous:

Mole crickets are not poisonous and do not bite people. While they technically could bite you if provoked enough, their bite would be completely harmless. Mole crickets are only harmful to your turf.

Source: Do My Own Pest Control

Good to hear, so we don't have to burn down our house just yet :)


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If we had children wear an apparatus swapping e.g. Red and Blue colors, would their perception adapt?
In the context of neuroscience and philosophy, one difficult question is what makes colors so peculiar and vivid if they're just signals encoding light intensity coming from certain receptors -- an instance of the "Problem of Qualia". In other words, why do perceived colors take their particular "qualitative" appearance. Experiments like color matching functions and simple mathematical properties clearly cannot fully account for this qualitative appearance -- a mathematical model like the opponent process:

can explain for instance that yellow and blue or red and green should appear to be in opposition, but it cannot explain exactly why we perceive green to be our particular green and not some other qualitatively distinct perception with the same mathematical properties.

1) Are the "appearances" of red, green and blue the only possible
  "appearances" that satisfy the mathematical properties of colors in
  our visual system? Or more generally are those simple mathematical
  properties plus their general relation to objects in nature sufficient
  to explain their subjective appearance? (say we had a propensity to
  like and perceive blue positively because of it's association with
  clear whether)

I suspect not. Intuitively I suspect there are a number of different ways colors could qualitatively appear like that go beyond this simple mathematical model and their association with seen objects, embedded in the structure of our brain's complex neural networks. But I don't have a convincing argument to support this conclusion.
I wonder what kinds of experiments can be done to explore this subject, and what experiments have already been done.
One such (imaginary) experiment that comes to mind is swapping different colors a child sees since birth with an ocular device. If the statistical association of objects and color signals were decisive for qualitative color perception, we might expect that then color preference (the favorite which is usually blue) would shift accordingly if we swapped red and blue -- people should start preferring Red over Blue.

2) Do we have any evidence suggesting the outcome of this kind of experiment (and the nature of perception in general)?

Your first question needs re-phrasing. Can you define "appearances" and "mathematical properties of colors in our visual system" more clearly? You insinuate that "appearances" are associated with preference, but surely that's not all there is to it, is it? The experiment you are suggesting sounds a lot like Mary the neuroscientist.

@vkehayas I'll think about it. Indeed my experiment is in the same vein of Mary the neuroscientist, but it has a big difference. I'm not questioning that physical processing gives rise to experiences with a phenomenal character (I'm assuming it -- I dismiss 'Mary the nsc.' since Mary). I'm questioning mostly why our phenomenal qualities are thus-and-so. Is the particular character of our experiences explainable solely by the visual system and what we see, or do we have to dive further into the brain for a complete explanation?

@vkehayas Also I associate "appearance" with preference, but I mostly mean that "appearance" should (weakly) imply preference: that Blue appears the particular way it appears to us would imply that most people like the color Blue the most -- which is empirically true; and not that preference fully describes "appearance". If preference changes when swapping colors (subjects prefer Red over Blue), that would be evidence that the appearance of colors is a function of the statistics of what we see -- that perhaps the "appearance" or "look" of nature has remained unchanged even with the swap.

But if preference remains the same, then it seems safe to conclude the appearance of isolated colors is independent of the statistics of our observations. That we don't like and perceive Blue in a particular way just because the sky is blue, or that we don't have a particular sensation associated with green just because trees and leaves are green.

"...or do we have to dive further into the brain for a complete explanation?": I think that this sentence, and the spirit behind it, is useful to include in the question. Your comments make what you are asking much clearer to me, so please consider editing the question to reflect those. I am unclear on the data concerning the preference to blue and would like to see a reference if you can provide it. Regarding the statistics of the environment and the preference to blue color:https://biology.stackexchange.com/questions/24481


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What is the difference between abundance and dominance in an ecosystem?
I was reading Hydroperiods of created and natural vernal pools
in central Ohio: A comparison of depth and duration
of inundation by Debra L. Gamble and William J. Mitsch (2008), and I came across this statement:

The dominant tree species in the vernal pool area were Acer saccharinum and Quercus palustris, while Ulmus americana, though smaller in diameter than the other trees listed, was the must abundant species...As at the New Albany, the most dominant tree species in the vernal pool area was Acer saccharinum, followed by Fraxinus pennsylvanica, while Fagus grandifolia was the most abundant species.

There seems to be a distinction between the terms dominance and abundance in the context of ecology. I've read some of the wikipedia articles on them, but I can't seem to find the difference in their meanings. They seem to both deal with the frequency that a species is in a population.
Any help is greatly appreciated.

There is a difference between dominance and abundance in vegetation science, and your citation is about vegetation.
Abundance is the relative representation of a species in a particular ecosystem. It is usually measured as the number of individuals found per sample.
Ecological dominance is the degree to which a taxon is more numerous than its competitors in an ecological community, or makes up more of the biomass.
In vegetation science, abundance is usually measured as the number of individuals or the percentage of coverage of that species in a plot. An abundant species would typically have a lot of individuals in the plot. A dominant species dominates the other species, so typically covers more than 50% (up to 100%) of the plot. Doing this, it also takes away space (and light!) for other plants.
Usually abundant species also cover a lot, but small species (for example grasses) can be abundant without becoming dominant while large species (like trees) can be dominant with relatively few individuals.

The terms are roughly the same, either is fine and you can choose depending on the audience or the nature of the topic and based on your preference.
A scientific journal examiner won't judge you for use of one or the other. Words outline ideas the same as color terms outline the rainbow, it's not very precise and two words can have similar and different meanings.
If you check the journal articles referring to species dominance and abundance, they are to similar to call a difference:
https://scholar.google.fr/scholar?as_ylo=2017&q=species+dominance&hl=en&as_sdt=0,5


text:
Building a PDB file from amino acid sequence of non-folded structure
I am interested in experimenting with folding simulations and algorithms for arbitrary sequences. I'm wondering if there is an easy way to convert an amino acid sequence into a PDB file for further simulation. To be clear I only want the primary protein structure.
If possible, I'd like to be able to characterize the bonds as well so that I can treat the molecule as a rigid body with rotational joints. Does anyone know something that can do this?

You may be confused about the terms. If you only want the primary structure you don't need a PDB file. There is no easy way to "convert" sequence into 3d model (PDB file), but the opposite is true - you can get sequence from a PDB file.

@marcin - I believe he does need a PDB file (or cif, or xyz, or whatever) as it would be an unfolded 3D model, with coordinates for all the atoms, but without a realistic geometry. As in fold.it, basically

yes, exactly @gilleain -- I want the 3D geometry of the unfolded model. It seems to me this is a relatively easy task since the geometry of the amino acids is known ... you just need to stack them together and preserve the peptide bond length. I'm just wondering if there is a library for this or do I need to write one.

@SalikSyed No, from what I know of there is no library that offers this description of a protein. I say this with a significant amount of confidence, as I myself just went through a similar search, and which resulted in me manually defining my own library, however, my library doesn't initially offer coordinate data, but instead, takes on a more topological perspective. It's written in Java, should you be interested.

Also, I would like to mention that PDB files specifically represent folded proteins, which includes 3-D coordinate data. Having this 2-D coordinate data is pretty much useless for the scope of interest and nature of research for most all scientists within this field.

So to be clear, it sounds like you want the 'coil' or unfolded structure of a protein based on the sequence?
There are plenty of programs out there to do homology modelling, which is taking a sequence of unknown structure and modelling it onto one with a known structure. On the other hand, there are many libraries for analyzing existing structures. What you want is somehow in between these two.
I'll add some links here as I find them:

There is a Lua library that might be useful : https://github.com/rob-miller/rFold
Modeller has functions for this: https://salilab.org/modeller especially this page
The Structural Bioinformatics Library : http://sbl.inria.fr/doc/index.html
The Rosetta library (as used in fold.it): https://www.rosettacommons.org/

I'm sure there are more, but it really depends on what programming language you want to use, or if you are implementing stuff yourself versus running some standalone software.

Thanks. Yes, I explicitly do not want the folded structure or to predict the folded structure via analysis or analogies to existing structures. I just want to convert the amino acid sequence into an unfolded 3D configuration of the protein where bond lengths are close to their average lengths. I want to then explore the conformation space solely based on perturbations to torsion angles (sample the energy for various configurations of the protein backbone) starting from the unfolded state.

rFold seems to be exactly what I am looking for, though I think I need to specify the relationships, native bond lengths and dihedral angles for each amino-acid manually


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Health effect of worm in Guava
I ate a ripe guava, rife enough to be broken with hand, i later saw that it has white worms with one black end crawling inside it, are these worm harmful, i had unripe guava of same batch though most of them had small black spot inside, but no worm crawling, what are these crawling worms, were they present in guava from unripe stage or infected only after ripening ?

Without photos it's going to be hard to even get close to an identification.

That worm inside the ripe guava is just the larva of a fly. I don't know where you are, but in South America the most common genus is Anastrepha. It doesn't make any harm eating a guava with them... well, except for the poor larva, which will die.

in  biology, human parasites never lay their eggs on fruit. a fruit and a human digestive system are not the same environment. the only other possible danger is chemicals in fruit dwelling animals. flies aren't very dangerous. but there are parastic flies like tsetse and the bot fly.

re fly biology: it would be interesting to see if the fruit is attracting the fly on purpose.  I am sure that the presence of the fly larva (meat!) increases the protein value of the fruit.  Maybe having larvae in it makes the fruit a tastier treat for an animal which can eat it and spread the seeds.

It is a safe bet that a "worm" as you describe in a ripe guava or any other ripe sweet fruit is a fruit fly.

from http://www.greenharvest.com.au/PestControlOrganic/Information/FruitFlyControl.html
Fruit flies are attracted to any ripe sweet fruit.  They are also attracted to vinegar and alcohol - both produced by yeast in and on the fruit, which is the high protein food that the fruit flies are really after in the fruit.
from
http://homeguides.sfgate.com/treat-fruit-flies-guavas-30550.html

When ripe, guavas emit a pungent, musky odor that attracts fruit
  flies. Fruit flies lay their eggs beneath the fruit's skin, and the
  maggots feed on the flesh. The damage causes guavas to rot. Fruit fly
  infestations often spread quickly, but prompt treatment can get
  populations under control.

The fly large actually speed the rotting of the fruit by moving yeast around on their bodies.


text:
Why is iodine solution a very effective and with a broad spectrum, bactericide, fungicide and viricide?
What is the similar property in each that allows a solution of iodine to deactivate and destroy so many species even from different kingdoms?

What research have you done before asking it here?

None, any guidance where to start ?

I'd suggest you begin with Google, and use reliable sites like Wikipedia (its usually reliable) or research sites like NCBI, Nature, Wiley, etc.


text:
Is there a biological term for an activity period that is determined by temparature
In general we refer to the activity period of organisms in terms of the period of the day that they are active.  Diurnal, crepuscular, nocturnal, matutinal, and vespertine, for example.
There are certain desert animals whose activity patterns seem to match a temperature range more than they do the day/night pattern.  Is there a term for this type of activity pattern?

I doubt there is such term.
Note that diurnal and seasonal are likely pretty well correlated with the temperature cycle. The temperature cycle is, I would presume, mainly affected by the daily and seasonal cycle.
You can talk about a behaviour that is dependent upon the temperature which fluctuates daily and seasonally. Looking for specific keywords on Google Scholar, it appears that most authors go through short phrasing of the kind to express this concept.


text:
What is the structural/chemical difference leading to different shapes in facial/head/pubic hair?
Different hairs have different shapes, thicknesses, properties.
What exactly is different between these types of hairs? a previous post implies that the root of the differing length (pun intended) is the rate at which the skin sheds the hair. However, this doesn't explain the different degrees of curliness, thicknesses, and textures.

hair shape texture is really easy. the biggest effect is the shape, size, and angle of the hair follicle. Hair with different cross sections have different properties. If hair is stiffer in one plane than other it will tend to bend along the weaker plane. Larger follicles will of course produce thicker, thus stiffer hair and the angle of the follicle can influence the hairs cross sections as mush as the follicles cross sectional shape can. Note the chart below is simplified triangular and kidney shaped cross sections also exist.

This is a nice picture, where did you find it?

Out of one of my lessons, let me see if I can find the original source. here it came from this forensics slide show. https://www.slideshare.net/leahmorgan/forensics-ch-5-6-notes

At one time I donated a "pinch" of head hair some years ago. A crossection was made with a microtome. The point being that there were many more colors that the photo above; white,black,red, and a dozen shades of tan/brown. My hair was nominally light brown. ( a much better photo also).

Similar to the differences between curly and straight hair, different hairs have different hair follicles.
Sex hormones at the onset of puberty rebuild the local vellus hair into terminal hair, which tends to be longer, thicker, and darker. The anagen/telogen/catagen cycle is different for these follicles and as a result they get longer.

you really should go into what differences their are in follicles.

As far as I can tell terminal follicles are just bigger?


text:
Why the C6 intermediate molecule in the Calvin cycle is so unstable
During the Calvin cycle, it is speculated that after Ribulose bisphosphate carboxylase/oxidase carboxylate ribulose bisphosphate, a 6C molecule is created and decomposed instantaneously into two phosphoglycerates because it is extremely unstable so:
Can anyone clarify why this molecule is so unstable? and...
how we know this molecule exists?.
I did not find anything useful while researching this, perhaps I'm not looking properly or there is no debate about it.

Please cite a reference for your assertion with date. On checking my copy of Berg et al there are full details of the reaction mechanism including the components of RUBISCO involved. I imagine it's a mixture of enzyme structure, chemical logic and experimental evidence, but you will need to go to the original papers if you want the details. There may be uncertainties, but if so it won't be alone. However RUBISCO has been intensively studied.

The question of why the molecule is unstable belongs to the realm of chemistry, which is not the subject of this list. Presumably the reaction for its hydration is thermodynamically favourable and there is a reaction mechanism which allows the reaction to proceed with a low activation energy.
The question of the existence of 2-carboxy-3-keto-D-arabinitol 1,5-bisphosphate and its role as an intermediate in the RuBisCO reaction was solved in 1986 and is no longer the subject of speculation. Its synthesis was described in a paper in Phil. Trans. R. Soc. Lond. B, which is behind a pay wall, but can be found in a post on ResearchGate.
In brief, they trapped this C6 compound in a more stable form with acid, and so could characterize it chemically. Its enzymic hydrolysis could then be studied at a slower rate.
The subsequent solution of the crystal structure of RuBisCO provided further confirmation of the reaction mechanism and molecular information on the role of the enzymic groups and magnesium ion cofactor. See, for example, the review by Gutteridge and Gettenby in Cell.
So the era of speculation would appear to be long past, and the account in standard biochemical texts such as Berg et al. — shown below — would appear to be reliable.


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Meaning of red blood cell volume expansion
In the scientific papers about EPO I read RBC volume (mL) expansion. What is it? The volume of a single cell or the volume expansion (=that is the increase of the number of cells) caused by the EPO?
Thank you in advance.
EDIT: see fig.1 page 3 please http://s000.tinyupload.com/index.php?file_id=08669957844938542361

Please provide context in the form of a citation from one of the papers together with a link. Otherwise your question is likely to be voted as off-topic because it is unclear.

Hi @David. See fig.1 page 3 please http://s000.tinyupload.com/index.php?file_id=08669957844938542361

Fine, by the place for this in your question. Please edit it accordingly.

Red blood cell volume is the percent of blood taken up by red blood cells (also known as the hematocrit), and is expressed as a percentage (so, normally, RBCs should comprise x% of blood by volume.) It says nothing of the size of the red blood cells.
That needs to be done by measuring the mean corpustular volume either by special machine or by looking at a slide of cells. So if the MCV is not mentioned, you can assume that expansion is referring to increased number of RBCs.
Smaller than normal RBC's are called microcytes, larger than normal are called macrocytes.
Recombinant EPO just increases the production of RBCs (and, unfortunately, it has some other effects as well.) It should not affect the size of the final erythrocyte.

Hi @anongoodnurse. If possible, can you link me some references about the sentence "It should not affect the size of the final erythrocyte." please? My unreliable professor said that EPO causes the increase of the size of RBCs. Thank you for your answer.

@GennaroArguzzi - I appreciate that you would like sources. I actually read a couple of papers about recombinant human EPO and in all the papers, it just discusses RBC volume, which is already defined. In none of the papers does it list RBC indices (that is, cell size, hemoglobin, the number of reticulocytes, etc.) If there's no problem (EPO has been used in dialysis patients for decades now) with the end result for erythrocytes (there are other problems: too many plateletts are produced as well, and a few other things), then it boils down to accepted terminology, as above.


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What is this plant/creature in my freshwater aquarium?

I've been noticing these really small creatures (or plants, I'm unsure) in my tank recently. They measure less than 1cm in length and I've only seen them at the bottom of my tank; some attached to the gravel and some to the glass. They have tentacle-like appendages on the end of their stem(?) and seem to drift with the with the water movement rather than on their own accord.
My tank is a planted tropical freshwater.
What is this plant/creature in my tank?
Any additional information on whether or not these are harmful to my fish would be appreciated.

coooool!  You are so lucky to have such cool creatures.  Feed them!

That is a hydra.
They are a kind of jellyfish, and as such they do technically have stinging tentacles. However, they're also very small, so they're not a danger to most fish or shrimp. If you're planning on breeding your fish they will eat fish fry if they get a chance. On the other hand some fish species will eat them, so it's a bit of a wash.
Generally they only thrive in tanks with extra food hanging around, so you may consider feeding a little less than you have been.


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Does a human body age at any place at the same rate or can there be big differences?
Aging can be caused by bad working mitochondrion, stacking of protein, shortening of telomers etc.
Now all our organs and materials have their own kind of cells, but are they equal vulnerable for aging by eating (which is the main cause of aging).
Probably there are some differences. For example the liver would get much more aged when drinking a lot of alcohol then one would get grey hair, because it is the task of the liver to break down toxic proteins etc.
But can in general be said that the aging of the body goes equal throughout the whole body, or are there more/many special patterns for each organ which are dependent on the kind of food is taken?
So for example a person can have very 'young' intestines but a very old milt or can a person get grey hair but all other organs are very young?

how do you measurably define aging? also you should have googled this first, there seems to be a bit of info on interwebz http://io9.gizmodo.com/scientists-discover-parts-of-our-bodies-age-at-differen-1449085569

So besides the causes I mentioned in my question also DNA methylation (epigenitic cause) is a cause of aging. But in general can be said : 'For the most part, the chronological age of our body parts matches its biological age. But there are some exceptions, including female breast tissue.'?

i suggest editing your question so it has two parts: this is what you know, this is what you don't or dont understand


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What insect is this
Saw many of these on my broccoli plant. Never saw them in the garden before today

I guess you live in North America?
Your broccoli is infested with the harlequin cabbage bug (Murgantia histrionica)
You took a picture of one of the nymphs.
Link to Wikipedia: Harlequin cabbage bug
To get rid of them, according to Wikipedia:
Handpick every bug and nymph off your plants.
Search carefully for eggs, which are black and white striped and come in packets of a dozen

Some excellent photographs! Garden pest or not, it's a delightful-looking creature.


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Name of this kind of stain on fruits and how do they form
Last year I made some photos with avocados touched by some stains. They were even more delicious than the regular ones.
What's the name of such stains and how do they form? My guess is that they form because the fruit was hurt but maybe that's just me.
Later edit: A farmer told me it's a disease. Then I've found that it looks quite similar with apple scabs. Is it correct to call this "Avocado scab"? Is it made by the "Sphaceloma perseae" fungus?
Here are the photos:

You never visited the avocado blemish identification fanpage? do you use google? it's quite good.
http://ipm.ucanr.edu/PMG/C008/m008fpfrtdmg.html
Causes of avocado Damage
Avocado thrips
Anthracnose
Caterpillars
Branch canker and dieback
Fruit and stem-end rots
Genetic mutations
Greenhouse thrips
Latania scale
Mechanical injury
Nutritional disorders
Off-season fruiting
Persea mite
Phytophthora fruit rot
Sooty mold
Sunblotch
Sunburn
Vertebrates
Weather extremes
Wildland fire
mosty they are insects, funghi, viruses, mechanical forces, and sometimes, like the woody avocado, the cause is unknown:

referenced.

Well, I guess each kind of damage looks different and distinct from the others, that's why I was asking what kind of specific damage is the one in the photos I referenced.

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


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Identification of fuzzy insect in Pennsylvania
I live in south eastern Pennsylvania, USA. About a month ago I came across this very peculiar insect. Its body was about an inch long, it was fuzzy, and it had a long proboscis(?) and long orange legs.  I've been wondering about it ever since. Can anyone identify it?

Related: What kind of red and black insect is in the photo?

This is the nymph of a bug (Hemiptera) from the Genus Arilus, probably Arilus cristatus, also known as "wheel bug".
Here is another image of it, for comparison:

Source: http://bugguide.net/node/view/288330
And here is the adult:

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


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Why Differential equation is not a good way to model chemical reaction networks
I'm a computer scientist and mostly code and have worked with Boolean models of cell level molecule transfer. Now i'm reading about the Biological pathways and modelling chemical reaction networks / Actions / Post translation modification and have no idea about differential equations.
What are the  pro's and con's of modelling these situations as differential equation Vs Boolean Vs Rule based approach.

Can you please clarify what you mean by these situations? The expression chemical reaction network is extremely broad and one cannot answer your question is such general terms. Also, it is unclear to me why you would consider by default that differential equations are "not good" to model "chemical reaction networks". The most famous equation in the field of molecular biology is Michaelis-Menten kinetic which result form a series of non-linear ordinary differential equations. I am voting to close as too broad.

Most respectfully speaking, if you don't know anything about differential equations, then an explanation of how they're used to model biology, to then perhaps implement into a program, won't do you any good. To study diff' eq's, you first need calculus I & II. However, to try to provide some kind of answer.. various branches of mathematics come with their own mathematical structures, just like various programming languages do. And, depending on what you wish to achieve, you will select a specific language/branch of math, to then utilize the structures & the features that come with them.

For example, in programming, linked lists are really good with inserting & removing elements in a collection. Sometimes this is useful, other times not so much. Well, perhaps with math, you may want to use differential equations in order to take on a continuous perspective when modeling your system, which has it's own benefits, like possibly being able to assume differentiation for an entire function. If you were to take a combinatoric approach though, of which is most often the mathematics of computer science, you may be able to utilize the features of a graph instead. It just depends..

I will say though that, at least from what I know of, every physical system we study can be expressed using differential equations (and most often is). There are of course many physical systems too complex for us to elegantly express, and so new & advancing research [in this branch of mathematics] is currently exploring difference equations & fractional calculus. That being said, you would highly, highly benefit from becoming at least somewhat knowledgeable of differential equations. Calc I & II, linear algebra (not necessarily needed but will help a lot), then differential equations.


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How did ancient human deal with biting insects like mosquitos?
How did early humans, once hairless, but before clothes and ointments.
I understand that hairlessness was an advantage against parasites but it it seems like a disadvantage antagonistic for mosquitos and such.

I believe your question is based on a wrong assumption: mosquitoes bite furry animals just fine. Having less hair doesn't seem to be a disadvantage against mosquitoes.


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Can an Ichthyologist identify this Canadian freshwater fish?

This will be very simple for a lot of you! But I been getting mixed answers about his catch. Is this a chinook salmon or brown spotted trout? Caught in Angus, Ontario, Canada. (Hwy 90 Bridge)
I appreciate the help!

Caught in a upstream river in Angus, Ontario (Hwy 90 Bridge)... Canada. This shot was from yesterday, Sunday sept. 17, 2017

Judging from the curved caudal (tail) fin, which is more square in brown trout, this appears to be a chinook salmon. The mouth also appears to be black whereas in brown trout the mouth is white.
Sources: Michigan Department of Natural Resources


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What is the definition of Mitotic Index?
Sometimes I find Mitotic Index defined as (i) the number of dividing cells over the number of non-dividing cells, other times as the (ii) the number of dividing cells over the total number of cells...
When reading a paper, which definition is more likely to be correct?

According to cancer.gov, it's the ratio of number of dividing cells to the number of cells not undergoing mitosis. This is equivalent to the number of dividing cells over the total number of cells.
Note that most papers, such as this one, report the mitotic index as a value from 0-100 (I.E. a percentage)

I might be missing something... but is it not the total number of cells = dividing (undergoing mitosis) + non-dividing cells (not undergoing mitosis)?

Yes, that's correct. A 1:1 ratio of dividing cells to non dividing cells would result in a mitotic index of 1/(1+1) = 50%.

The answer is slightly misleading, as "dividing cells" can refer to cells being in cell cycle (as opposed to G0 / senescent state), whereas the mitotic index refers to cells "undergoing division" (cancer.gov), which refers to cells where the material is currently being divided to two different daughter cells - which corresponds to the "mitosis" cell cycle phase of dividing cells.


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Do plants use only solar energy or can they get energy from other forms of light?
Plants use energy from sun. Is it just sun's light energy or any form of light (like light from a tube light) can excite electrons and initiate photosynthesis.
This actually sounds a bit idiotic but in Campbell Biology 10th ed. there is a line in Ch 4. "Plants use solar energy to convert atmospheric CO2 to molecules of life...."
If it is due to sun, then how does plant know which light is from sun and which is not?

Plants use any light of the proper wavelengths. The sun provides a lot of light, but think of covert/indoor plant growing: the right bulbs (and enough of them) allow the plants to grow strong.

@anongoodnurse I think, you could make an answer out of your comment.

@Remi.b - I don't mean to sound unkind to the OP, but I think it's pretty common knowledge.

I don't think we should refuse questions because it feels too introductory to us. When not knowing the answer to such question, it might actually be hard to look for it so I don't think it shows lack of effort. I'll just answer it using your comment if you don't mind.

As per @anongoodnurse comment:
Plants use any light of the proper wavelengths. Typically the available light to plants is the sun but if you place a plant indoor under a fair amount of light bulbs that produce light at similar wavelength that the sun, there is no reason for the plant to even notice the light is different that the sun light and the plant will grow just normally.


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Can you Interrupt a promoter region by inserting another promoter region into it?
I currently have a plasmid (pFPV25.1) which contains a promoter region with multiple cloning sights in it. I would like to place a new promoter I have isolated, and I was wondering whether I could  insert the new promoter into the middle of the old promoter; would that result in the new promoter controlling the gene of interest?
What I understand is that the RNA sequence that would be transcribed will change, but the start codon for translation would be kept consistent by doing this method, resulting in the gene being controlled by the new promoter.
Thanks.

If you're trying to study the new promoter, you should probably remove the old one completely. There should be restriction sites outside of the MCS that you could use to cut the old one out and insert the new one.

If you do choose to insert the new one inside of the old one, you should find a way to convince yourself (and the reviewers) that the old one has in fact been inactivated by the insertion.

Ok, I will sequence the plasmid would this be enough? What protocol would you recommend.

I'm not saying that you need to confirm that the insertion has taken place but rather confirm that the insertion completely abrogates activity of the old promoter. I'm entirely unfamiliar with the plasmid and promoter that you are using, so it may be that this has already been done and reported in literature. However, if this is something new you are trying, you need to show that expression is controlled entirely by the new promoter and not some residual activity of the old promoter, or at least rationalize that that is the case based on the nature of the old promoter and the insertion site.

The new promoter that I am using should only be activated in the presence of a heavy metal. The other one is activated all the time. Thus, once I do insert into the plasmid, and no GFP is seen to be produced  then this confirms that the previous promoter have been destroyed.

of course, not in the presence of a heavy metal

That would be quite convincing. However, can you be sure that elements of the old promoter don't interact with the new promoter? Again, I don't know anything about the promoter and so this may not be an issue. I'm just trying to think of potential problems.

agreed. Its not the best idea


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Frog in Akaka / Loango Région Gabon
I was recently in Gabon, and I did some long and serious treks with Pygmées into some forest mostly to see Chimps and Gorilla around the Akaka area in Loango national park.
During a trek in forest I took a picture of this frog, it's been a little while now I can't find the exact species of it.
Any ideas guys ?

https://ibb.co/eU4ROk Full sized picture here

I'm not completely sure as it's very difficult to determine frog species with just one picture taken from the side.
Morphology-wise it looks like this is a Afrixalis dorsalis, although it's colour doesn't comply with the most comomon pattern. You can find pictures of this species with specimen looking exactly the same or very similar.
Colour deviations occur in several frog species...
interesting article about frog species in Gabon
AmphibiaWeb Afrixalis dorsalis (this also mentions differences in patterns and light coloured populations)

Source: Wikimedia Commons

Source: http://calphotos.berkeley.edu

Common colours and pattern
Source: http://calphotos.berkeley.edu

Thanks for your answer, true the morphology looks like afrixalis dorsalis, might be it ! Just could not find that pattern with the black strip from the eyes to the nose and also that little shiny yellow on the top of the eye. Could be a variation.


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Why there is replication of DNA before meiosis?
It seems to me that, even without replication of DNA before meiosis, the homologous pairs can still do crossover, and then be pulled to opposite poles, directly forming 2 haploid gametes.


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Why HIV need integrase enzyme to integrate their DNA into host cell?
In gene transfer by microinjection, the gene of interest is injected into the nucleus of host cell without using integrase enzyme. So why does HIV need that enzyme? Why they not just place their DNA into the nucleus and let it stay there?

During gene transfer by microinjection the DNA has at least some fragments of identical DNA sequence to the host genome. Usually DNA that is used for microinjection will have flanks on either side identical in sequence to two nearly situated, sometimes adjacent blocks of DNA sequence. This allows homologous recombination to occur which engages proteins already present in the host cell: https://en.wikipedia.org/wiki/Homologous_recombination
In case of HIV, there are no fragments of identical sequence flanking the genome of the virus, so no homologous recombination can occur, therefore integrase is necessary. Furthermore, integrase inserts viral genome into random parts of the host genome unlike homologous recombination, which would always localize that viral genome into the same spot each time.
Now, this is my wild guess, as I couldn't really find any evidence in the literature but I'd say it gives the virus certain advantage. Site-specific insertion could be easily inhibited in the course of evolution by mutations within the host genome and eventually the virus would be eliminated. This is not the case with random allocation, as no mutations in the host genome will ever substantially change the probability of integration.
Here is a good review on the process of DNA integration regarding HIV: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3385939/
Let me know if this helps, confront your opinions with what I think.
Cheers,
Krzysztof


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Does neural oscillation happen at the same frequency in all parts of the brain simultaneously?
Does neural oscillation happen at the same rate in all parts of the brain at a given time?
I'm trying to learn and understand about brainwaves, and I know about the various categories of brainwave. Therefore, my question is are all parts of the brain firing off at the same frequency at any given time or are some parts for example operating at a delta frequency and others operating at alpha frequency? Do different types of brainwave occur simultaneously or is always all of the brain operating at one frequency?

Neural oscillations occur on both a cellular level and on a macroscale level, the latter usually referred to as brain waves.
Looking at macroscale brain activity and particularly brain waves is often done via EEG, which has poor resolution and suffers from attenuation. EEG activation is really due to huge numbers of neurons. Hence, it represents a very coarse, averaged view of the current activity. So, even when the EEG shows nice smooth variation, the individual neurons are far from it! Of course, more recently, using other methods (e.g. fMRI) has become more common.

My question is are all parts of the brain firing off at the same frequency at any given time or are some parts for example operating at a delta frequency and others operating at alpha frequency? Do different types of brainwave occur simultaneously or is always all of the brain operating at one frequency?

No, as I said, most studies look at the cortical areas specifically. But even within the cortex, the brain activity is very complicated, and certainly not subscribing to any one frequency. (In fact, when this hyper-synchronization happens, it is called an epileptic seizure! e.g. see Garcia-Hernandez et al, Understanding synchronization and hyper-synchronization in the the septo-hippocampal system).
In any case, imagine brain activity being measured over time. We then look at the frequency components (e.g. via Fourier analysis). See e.g. Gross, Analytical methods and experimental approaches for electrophysiological studies of brain oscillations for details. Notice these methods usually give the "strength" of the activity across the frequency spectrum. When there are brain waves, we are merely saying that activity is concentrated in a specific frequency band. It is often smeared across the band, and activity usually exists throughout the spectrum.
It also depends on spatial resolution of the frequency analysis. Some studies look at, say, just the Hippocampus. So yes, it is quite possible for some of the brain to operate at one frequency, while others operate at another. Or one could average over the whole cortex. It depends on the study!
So pretty much in all cases, everything is more heterogeneous than you might think.
Some literature to read:

Breakspear, Dynamic Models of Large-Scale Brain Activity
Varela et al, The Brainweb: Phase Synchronization and Large-Scale Integration
Salinas et al, Correlated Neural Activity and the Flow of Neural Information

Top answer. Cheers :)

As the question mentioned "at any given time", I would like to add that activity in a certain frequency range for a specific region is not constant.


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Is it necessary for spiders to both wrap the prey in silk, and inject them with venom?
I stumbled upon the following paragraph on the Wiki page about Argiope bruennichi:

When a prey item is first caught in the web, Argiope bruennichi will
  quickly immobilise its prey by wrapping it in silk. The prey is then
  bitten and then injected with a paralysing venom and a
  protein-dissolving enzyme.

On hindsight, it seems a bit redundant to do both those things. If prey is caught in the web, which is rather sticky and therefore restricts its movement, isn't it possible for the spider to go right ahead and inject venom?
Or on the other hand, if it wraps and immobilises the prey in silk, wouldn't it be more logical to then leave it to die, from some sort of evolutionary standpoint of wanting to saving energy and resources?

Nice question!
Based on some previous observations on other web spiders, I belive that these "redundant" behaviors are selected to avoid prey scapes, and are not trully redundant if we remenber that some preys are able to evade even if wraped. Some beetles can find a way out from the web, moving their strong legs with projections, eventually some silk lines are cut. Also beetles are more protected against bites then are other bugs, since many are under their natural armor.
Other possible explanation** :some bees, ants and wasps produces chemical signals when in trouble, attracting their sisters. From the spider point of view, this could be a way to get more food. But too many of these insects could possibly destroy the web, only because their are numerous. Obviously these are speculations.
Also, some wasps prey on web spiders. If the wasp eventually touches the web and entangles itself, now the wrap/bite strategy turns in defensive way, maybe with the "danger turns dinner" bonus.
 I did not search too much, but probably someone has alread tested some of these possibilities. Also, I read once that some spiders can treat distinct preys in distinct ways, even releasing some undesirable bugs from the web.
** This bee-wasp-ants-hypothesis is not based on observation, only on knowlodge about insects and spiders.


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Will "circus peanuts" biodegrade, and how?
I have a compost barrel, and it is currently staffed by black soldier fly larvae. They eat pretty much anything, which is very satisfying to observe. I put a handful of the candy known as "circus peanuts" in there, and they haven't touched them so far. As you can see following the link, the ingredients are:

sugar, corn syrup, gelatin, pectin, soy protein, food coloring, and artificial flavor

I assume these things are biodegradable, being "food", but if my star decomposers won't eat them, then what will? What can I expect to happen to these items in the compost heap?
As a follow-up question, was this a bad idea? Should I take them out and throw them away, so they can rot in a landfill instead?

The lack of moisture in them is probably the main difficulty. You might try crushing one so that moisture from the rest of the compost can enter it.

Time answered this question. I didn't do anything to the candies, but moisture eventually worked its way in. After a week or so, they were showing definite signs of breaking down. After two weeks, I couldn't see a trace of them!


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Which spider is this? Is it dangerous?
So today while clearing the trash out of my room I found this orange spider on an abandoned piece of foam.

 It is carrying a weird ball with it wherever it goes. What is this? And to which genus does this spider belongs?
For a better contrast I placed it on  paper.

EDIT-1
Size: Roughly 1cm in length
Location: Uttar Pradesh, India. Coordinates- https://maps.app.goo.gl/svXoxaH4Z2lK2rFH2
Temperature: 34°C and Humid.
EDIT-2
Adding few more pics

It is clearly a Theridiid (cobweb) spider, but it doesn't look like the Parasteatoda tepidariorum I'm familiar with here in the US.  The egg sac it's holding indicates it's a mature female, and the regular pattern on the abdomen is both distinctive and unlike the variable, blotchy pattern of tepidariorum.  Unfortunately, not being familiar with Eurasian spiders likely to be found in your area, I can't be of much help as to what it might be, beyond limiting it to the Theridiids.
Oh, yes - it's pretty clearly not one of the Widows (Latrodectus spp.), and since those are the only medically significant Theridiids we know, it's not dangerous.

https://en.wikipedia.org/wiki/Parasteatoda_tepidariorum
I have personally come across these little spiders at my place and they look very similar to the Parasteatoda tepidariorum.

Can you add an image, check whether its distribution includes India, add a little background why you think it is this species  etc? We discourage one-liners

@AliceD I am sorry as this was meant to be a comment but was not able to do so because of the reputation policies that encourage to write answers when you are new.


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Can you say "screening for a" in English?
I know this is not a "Correct Use of English Forum" but I'm afraid that people from outside the field won't be able to properly answer my question.
Would it be correct to say "screening for a long peptide capable of killing Gram-positive bacteria"? Or you just have to turn the word "screening" into a noun like: "preparing a screening for a long peptide capable of killing Gram-positive bacteria"?
The last one doesn't seem right to me at all, but I'm not sure since I'm not a native speaker :(
Thank you for your time!

There's nothing evidently wrong with your first option. Your second option could read "preparing a screen for…"

"Screening" can be a verb here ("we screen for the long peptide") so your first sentence would be correct.
Even in this biological context this might still be a question better fit for the English/Learning English forums though.


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Does pre-operational exercise affect recovery from surgery? Statistical Analysis
https://www.medicaljournals.se/jrm/content/html/10.2340/16501977-2210
I understand the difference between statistical significance and effect size, but I am having trouble interpreting the data on Table III in the article linked above. I am evaluating the WOMAC scores. My first question is can effect size confidence intervals cross zero and still be valid? My second question is about the negative and positive values of the Hedges'g. The first study scores the WOMAC in a way where the higher the score, the better the outcome. The second two studies score the WOMAC in a way where the lower the score, the better the outcome. Does this mean that in the first study a positive Hedges'g indicate larger effect for the treatment group and a negative Hedges' g for the other two studies indicate larger effect for the treatment group?

I think is a question for another section of the community, the statistical one: Cross Validated

Welcome to Biology.SE. I'm voting to close this question as off-topic because it belongs to stats.SE (or at worst Health.SE but definitely not Biology.SE). +1 to @vkehayas answer though.

Also, please always narrow your posts down to a single question.

Regarding your first question, the effect size is not invalid if the confidence interval (CI) crosses 0. The effect size is a point estimate. When the CI -a range estimate of the coverage probability- includes 0, the probability that the range of the effect size can include 0 cannot be rejected at the $1-\alpha$ level of confidence.
Regarding your second question, from the definition of Hedge's g:
$$g = \frac{\bar{x_1} - \bar{x_2}}{sd_{pooled}}$$
we can see that if $\bar{x_2}$ is larger than $\bar{x_1}$ then $g$ will be negative. So, the sign only determines which of the estimates is larger and that will depend on which estimate is considered as the reference.


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Species richness corrected for area -- should area be log-transformed?
I am doing a study to compare plant species richness (total number of species per site) to a bunch of environmental factors of sites at which these plants were surveyed. Because these sites are different in size, I have converted species richness to a species density measurement by dividing by the log of site area (species density = species richness/log[area]).
I log-transformed area, because the relationship between species richness and area at my sites is linear on a semi-log scale. Now that I have calculated species density in this way, I am having a hard time convincing myself that calculating density with log(area) was the correct approach. Does anyone have some insight on this? My community ecology background is not strong and I am getting bogged down in the literature.
Thanks!

related: Can I compare Shannon-Wiener diversity indices between plots of different sizes (area)?

Let me offer my answer even though I have not worked in ecology.
You are asking two questions if I understand you correctly:

Should you normalize to the area sampled?

The answer to that depends on whether the area sampled is a nuisance variable or not. Is it the case that you just happened to sample from areas with (largely) different sizes? Or do you rather expect or are interested in whether it may display some interaction with the environmental factors that you study? In the first case, normalize with clear conscience. On the latter, you should probably include the area sampled in your model. The reason for this is that by normalizing, you are assuming that the relationship between the response variable (number of species) and the predictor (area sampled) is fixed and has a slope of 1 irrespective of the variation of the rest of the variables included in your model. If that is not the case, you want to explicitly add the area sampled as a fixed factor in your model.

Should you log-transform the area sampled?

If the answer to the first question is that the area sampled is a nuisance variable then it does not matter whether you log-transform or not as now you are interested in a new measurement, species density. Hence, you may work with the untransformed variable which would simplify the interpretation of the results by a tiny bit. If the answer to the first question is that you want to investigate the interaction of the variable 'area sampled' with your other predictor variables, then you do not need to log-transform your variable as this is rarely needed, even if you use parametric inference. To summarize, you do not need to transform the variable 'area sampled'.

If the relation between species richness and area is linear on a semi-log scale (as the question states), wouldn't it be best to include log[area] in your model ?

Assuming that you will use a model with a linearity assumption, you don't need to transform the predictor variable. It's only a matter of taste for the interpretation of the results. The most common variable to transform is the response variable, if needed. But I am assuming that this follows a discrete distribution like poisson. So you wouldn't perform a linear regression but a poisson regression. We would need more details about the analysis to say more.

If you choose to study species density, which will follow a log-normal distribution as I understand, then you will probably need to transform the species density response variable, or use a GLM with a log-link.

I think that the latter will be the case. However, I am beginning to wonder if this question shouldn't be migrated to stats.exchange...

The important factor of the question on whether to normalize or not is a biological question (see my point 1). Regarding log-transformation of a predictor variable you will find many (potentially duplicate) posts in stats.exchage, including the one I linked.


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Can a crowded mitochondrial membrane limit O2 uptake?
The mitochondrial inner membrane is crowded with proteins (electron transport chain complexes, ATPases, etc.). As the proteins are packed more and more densely in this membrane, the diffusion of any molecule through the membrane should decrease, since there are less "gaps" for it to go through. I have no idea if this effect is insignificant for the entry of O2 into the mitochondria.
So my question is: Can O2 entry into the mitochondria become limited due to the high density of proteins in the mitochondrial inner membrane?


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Rapid Decomposition Of Fruits & Vegetables During Hurricane
A very strange thing (To my mind) has just happened in my home. On the eve of Hurricane Irma, I purchased some food including cucumbers and grapes. I left them in my kitchen area overnight. When I woke up the next day, the hurricane was overhead. I went into the kitchen and noticed a large puddle of water on the floor that smelled of cucumber. The bag I had left the cucumbers and grapes in was at the center of this puddle.
I opened the bag and saw that the cucumbers and some of the grapes had completely disintegrated. It wasn't as though they had decomposed in any normal way. There was no visible fungi and the cucumbers didn't look especially rotted, just mostly gone. Only a small portion of the cucumbers remained. Many of the grapes were in a similar state.
How is this possible? When I bought this produce, it was fresh, not old. They had been reduced to almost nothing in less than 24 hours. I tried researching possible causes for rapid decomposition but normal decomposition of a cucumber (To this point) takes several months. I wasn't able to find a single article or time-lapse that reflected my observation. I've always been very interested in mycology so I set out to find a fungus that might be responsible but I have as of yet been unsuccessful. Could the pressure of the atmosphere during the hurricane have played a role?
If anyone can explain this, I would love to know what happened. Do I have some rare fungi floating around my house? Should I be worried?

If possible, can you kindly include a picture of the grapes and cucumbers?


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Mitochondria - ETC
I read somewhere that the Malate aspartate shuttle transfers the electrons to complex 1 in the ETC while Glycerol phosphate
shuttle uses complex 2. Does anyone know if this is true? Also a lot of textbooks state that complex 2 can bypass complex 2. Does anyone know if this is true? I have seen this statement in the book Biochemistry by Voet and Voet.

Hello! thank you for the answer. But do you know if it is possible for these two complexes to bypass each other?

Thank you. Please let me know if you have any references for this above mentioned bypassing.


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Grasshopper identification
I found this grasshopper (although I'm not sure if it was really one) near a lake in Bangalore, back in mid April. This is the only picture i could get and since it's so well camouflaged I would like to point out that it's right in the middle. It had those very conspicuous green bands on either half of the dorsal side with longitudinal white pinstripes. It was around 10 cms in length. Can i get an ID please?

What's meaning of get an ID?

@aircraft The OP is requesting that someone provide the taxonomic identification of the grasshopper.

This is known as a "long-headed grasshopper", and belongs to the species Acrida sp. Of the species I've been able to find images of so far, I think is most closely resembles
Acrida conica

and
Acrida bicolor

A full list of species for this genus can be found here.

@AdDate You're welcome! I'll keep trying to find an aerial view that more closely matches yours.

I think it might've been an Acrida bicolor . There is a good ariel view on Wikipedia but I can't seem to upload it. Could you confirm?

@AdDate I think it's close, but still not the right species. The bicolor definitely has the white streaks running down the body, however, it lacks other dominant patterns, such as the green gradients and thick, white trim, which is heavily demonstrated in your image. The reason why I suggested the A. conica was because it does carry this thick white trimming, and does show some streaks. But it does still lacks the gradients though, which would be characteristic of the true species, I believe.

I highly doubt it's A. Conica. That species is mostly found in Australia and New Guinea. I don't think it is found in India.


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History of ideas about the form of the genetic code
In preparing a lecture on mRNA translation and the genetic code, I remembered a talk given at a symposium where they mentioned the origin of the code and how, before the code was established, various other mathematical possibilities were proposed that turned out to be incorrect.
Does anyone know about these alternative proposals?

The Nobel Prize speech of Marshall Nirenberg maybe interesting: https://www.nobelprize.org/nobel_prizes/medicine/laureates/1968/nirenberg-lecture.pdf

Before it was established that there was a triplet, non-overlapping, comma-less genetic code* for what at that time were thought to be only 20† amino acids, there was uncetainty about:

The codon size (must be more than 2, but...)
Whether the codons overlapped (e.g. in a stretch ABCDEFG with triplet codons, whether ABC, BCD, CDE etc were the codons)
Whether there were ‘commas’ as demarcation betwen different codons

These and other problems were disscussed by Crick et al. in Nature (1961) 192 1227–1232. There is an introductory gloss of this on Scitable, with a link to free-view of the original paper.
Footnotes
*We now know there are variants on the standard genetic code, but all the codes have the characteristics mentioned.
†In addition to the standard 20 amino acids stop codons can be subverted in certain circumstances to encode selenocysteine and, in some bacteria, pyrrolysine.


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Can streptavidin be conjugated with EDC-activated carboxylates?
Recently I conducted an experiment to conjugate amine-modified oligonucleotides with hydrogel particles having carboxyl groups. However, the fluorescence (from hybridized FAM-DNA) only appears on a small area of the particle and its shape is this ill-defined, like in the image below.

My advisor said that "DNA is negative charge and carboxyl group also have negative charge so there is no possibility of conjugation, conjugation of streptavidin to particle, attaching biotinylated DNA and proceed with hybridization".
However, conjugation using NHS / EDC requires both an amine group and a carboxyl group. Does streptavidin have the requisite chemical groups to do such a conjugation? Streptavidin is Sigma Aldrich's 85878 (Streptavidin of Streptomyces avidinii, affinity purified, 10 mM potassium phosphate, lyophilized product of ≧ 13 U / mg protein).
PS: Please tell me if there is a secret to make it conjugate evenly on the surface.
PPS: We use 5 μM anime modified oligonucleotide and 100 nM FAM-DNA.

I really don't get why this question had a downvote.

The EDC-activated carboxylate is actually positively charged, though I cannot speak to the density of carboxylates in your hydrogel or the extent of activation with your protocol. Subsequent NHS activation generates a negatively charged adduct. If charge repulsion is an issue during coupling, you can try experimenting with salt concentration or adjusting pH around streptavidin’s isoelectric point (but keep in mind that the reactions themselves also have a pH optimum).
Streptavidin has plenty of primary amines (lysine and N-terminus) to react with EDC- or EDC/NHS-activated carboxylates, and is routinely conjugated to carboxylate functionalized resins. As streptavidin also has carboxylate groups, it may be desirable activate the resin first and then conjugate streptavidin to avoid unwanted side-reactions.
You can read about the EDC/NHS reaction mechanism here (ThermoFisher).


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Cyanobacteria: Gram negative or Gram positive?
My (school) textbook states that cyanobacteria ("blue-green algae") are Gram positive (no references provided). They mention this at several points over the chapter we're doing so it doesn't look like a typo.
However, this Wikipedia article on "Gram staining" (under "Gram negative bacteria") states:

Gram-negative bacteria generally possess a thin layer of peptidoglycan between two membranes (diderms). Most bacterial phyla are gram-negative, including the cyanobacteria, spirochaetes, and green sulfur bacteria, and most Proteobacteria (exceptions being some members of the Rickettsiales and the insect-endosymbionts of the Enterobacteriales).
 Emphasis, mine.

There is no mention of cyanobacteria under the section "Gram positive bacteria".

I understand that there is a possibility that some cyanobacteria stain positive, and other stain negative (owing to the lack of a very sharp definition for "cyanobacteria", as well as the limitations of Gram-staining).
So what I want to know:
1) Are cyanobacteria generally Gram positive or Gram negative?
2) Are there exceptions to that general trend? If so, what are they?

Cyanobacteria are clearly didermic (two membranes, inner and outer) bacteria, normally classified as Gram-negative bacteria. If your textbook says several times that they are Gram-positive, instead of a typo, you have a plain mistake.
However, things are not that simple.
According to Hoiczyk and Hansel (2000), this traditional classification of the prokaryotic envelope doesn't work well with cyanobacteria, whose cells show a combination of the features of Gram-positive and Gram-negative bacteria:

The multilayered peptidoglycan of gram-positive bacteria, with a thickness ranging from 20 to 40 nm, usually forms a physical barrier for the dye. In gram-negative bacteria, however, with their relatively thin sacculus of 2 to 6 nm, the stain can easily be washed out. Together with other characteristics, such as the occurrence of accessory cell wall polymers or the presence of an outer membrane, the peptidoglycan architecture largely determines the different properties of the two cell wall types in terms of mechanical stability, permeability, and resistance toward chemical substances. Although this classification is generally useful, it oversimplifies the concept of bacterial cell walls. It also ignores, for example, that the largest and perhaps most diverse group of bacteria, the cyanobacteria, possess cell envelopes with a combination of these features. (emphasis mine)

Here is an image (ibid.) comparing a Gram-negative cyanobacteria with Escherichia coli:

Electron microscopical comparison of the gram-negative cell envelopes of the cyanobacterium P. uncinatum (A) and E. coli (B). Both bacteria were identically processed using cryosubstitution procedures. Note the combination of gram-positive and gram-negative features present in the cyanobacterial cell wall, like the thick peptidoglycan layer and the outer membrane, respectively.
Hoiczyk and Hansel (2000) add that...

... Despite their overall gram-negative structure, the peptidoglycan layer found in cyanobacteria is considerably thicker than that of most gram-negative bacteria. (emphasis mine)

In conclusion, cyanobacteria are Gram-negative bacteria. However, their envelope show some features os Gram-positive bacteria. Besides that, there is variation withing the group.

Source:

Hoiczyk, E. and Hansel, A. (2000). Cyanobacterial Cell Walls: News from an Unusual Prokaryotic Envelope. Journal of Bacteriology, 182(5), pp.1191-1199.


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Does evolution go only in one direction?
In this video Richard Dawkins talk about intermediate fossils. He describes how the whales were evolved from a common ancestor who lived on land.
But his theory sounds more like a devolution. I thought evolution was coming from the sea to the land and then to the skies. Are there more examples where species evolve back and forth between the ocean and land or skies?

If you change your thought of evolution to mean "getting better" to simply "changing", it becomes clear that loss of function in exchange for another is really no different than gaining function from nothing.

Does evolution go only in one direction?

No, it does not. There is no such thing as a goal of evolution at making things fly or at making things intelligent or whatever. There is no intrinsic directionality.
In short the reasons are 1) Evolution is much more than just natural selection 2) natural selection does not systematically select for a specific trait. Some traits are advantageous under some ocnditions, some other traits are advantageous under other conditions.
I won't talk more about the mechanisms of evolution here as it would take a whole book. Instead I will recommend a source of information for you to further your knowledge.
Source of information
As your question is very introductory and shows misunderstanding, you might want to have a look at an intro course to evolutionary biology such as for example Evo101 by UC Berkeley.
Devolution
Note that this term is rarely used in the scientific literature (actually I think I have never encountered it in the scientific literature). From wikipedia:

In modern biology the term [devolution] is meaningless: evolutionary science deals with selection or adaptation that results in populations of organisms genetically different from their ancestral forms, where evolution has no intrinsic directionality. The discipline makes no general distinction between changes leading to populations of forms less complex or more complex than their ancestors, and in such terms the concept of a primitive species cannot be defined.

The question is a bit unclear
There is a slight issue with the question as it is not that easy to categorize all animals as living strictly in the water, on land or in the sky. Note that almost no living things live strictly in the sky without ever touching the ground. Here are a few examples of limit cases

oysters
dragonflies (larvea live in the water, adult fly)
flying squirrels
Most ducks (spend much time on water but nest on land)

As a consequence the question is very undefined
Examples of potential interest to you
The question is undefined but here are a few examples of cases anyway that will interest you. For simplicity, I will reduce my list to animals only and will not consider similar cases in procaryotes, and non-animal eukaryotes such as plants and fungi.
Whose ancestors were terrestrial

Cetacea (blue whale, orca, dolphins, ...)
Sirenia (dugong and manatees)
Pinnipeds (sea lions, sea leopards, ...)
Monotremes
Marine iguana (and other swimming lizards)
Beavers
Otters

Whose ancestors were flying

Penguins
ratites (Ostrich, emu, kiwi, ...)
dodo
Many birds are able to stay for relatively long period under water when hunting for fish.
Ants and other non-flying hymenopterans.
Ground beetles and other non-flying beetles
water beetle

Again, categorization is not that easy. I just want to highlight the water beetle as example where the ancestor was marine, then terrestrial, then flying, then non-flying and finally living in the water again.
Related post
How many times did terrestrial life emerge from the ocean?

It is still hard for me to believe if I start swimming in the water and all my offspring also they will eventually start growing fins. Down the road, someone will develop something like it. How will that get introduced into their DNA? Shouldn't we be able to see in DNA if changes like evolution are possible in DNA? Mutations do not follow the outside pressures or need but they are just errors in the system.

@Grasper: DNA isn't really as straightforward as you seem to think.  There's not a simple mutation for "fins" vs "feet", but different genes being expressed differently.  Consider phocomelia, a condition where factors like pre-natal exposure to a drug produces flipper-like arms & legs: https://en.wikipedia.org/wiki/Phocomelia  Then any mutations are selected for or against from a population of millions over thousands of generations.

@Grasper You are right to have a hard time to think that your direct offspring will all of sudden and out of the blue grow fins if you swim a lot. But this is not what the evolutionary theory is claiming. I won't give you a whole intro course to evolutionary biology because it takes a lot of time and many other people have already done so.

@Grasper Please just have a look at an intro course to evolutionary biology and you'll understand a little bit of what evolution is about. As recommended above, you might want to have a look at Evo101, a very short and very introductory course to evolution.

Evolution helps an organism to be successful in the environment in which it lives. In this case, the organism evolved to suit it's aquatic environment. So there's nothing called devolution. For example, the cave  proteus is blind while it's ancestors weren't. It does not mean that it has devolved. It doesn't require well developed eyes in a dark cave. So it has evolved to suit it's environment. Same case here.

Isn't that called adaptation?

Welcome to Biology.SE! Please add some more details and references in your answer.

Adaption gradually leads to permanent changes...which is evolution. The most favourable,adapted character passes on to the next generation and it leads to evolution. Adaptation and evolution are mutually inclusive events.

You do not seem to fully understand the definitions of evolution and adaptation. In the future, you might want to answer question in the fields in which you have at least some intro knowledge

Is there any reasons for posting two independent answers rather than just expanding on a previous answer? Note that you can use the "edit" button to edit an existing answer.

Oh. Can you help me with that if possible? I'll be really happy to gain some knowledge

@Remi.b  I'm new to stack exchange! Thanks man!

No worries. I'll be happy to take some time to answer a post you may want to open. Asking a clearly defined question can be challenging (and it is not uncommon for new users to see their post getting closed), so it may be good to start with an intro course and build from there. As recommended to Grasper, you may want to have a look at Evo 101. Welcome to Biology.SE (and other SE websites) and Good luck!


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Moth identification
This moth was found lying on the road in Bengaluru, India. Although it was damaged very badly from the under side, the wing pattern was still intact. Is it still possible to identify it?
It is 9cms from head to wing tip

Hi, the identification process is easier if you can tell us a bit more about it. It's better if you can provide an image without a flash (no bright light either). Where was this bug found (country, state, etc.)? How big is it?

Oh yes I'm sorry I forgot to mention, it was found in Bangalore

I have inserted a new picture taken under normal lighting conditions. Thank you for pointing out the error @Aravind Suresh

This is a hawkmoth, Sphingidae. One of the largest and arguably most beautiful of all moths. I am not familiar enough to  India to pinpoint the species, it might be a member of the genus Agrius or Manduca.
Here's a picture of a resembling, species from the Manduca genus.

https://en.m.wikipedia.org/wiki/Manduca

I myself had thought of a hawk moth, however, I didn't think the wing pattern was consistent with the OP. Can you explain to me some of the resemblances? Thanks.

@Charles the forewing is much longer than the body and covers the (hence much smaller) hindwings.  The forewing is also strongly curved towards the tip. I can't think of any other genus with this shape&size, but am open to learn something! The wing pattern is quite worn, at the tip of the left wing you can see through. That makes thw wing pattern less reliable in this case.

This isn't a hawk moth; the forewing venation is not correct for that family (it is possible to see that two anal veins reach the wing margin in the OP photo; compare with figure 5 on page 5 here; the veins aren't labelled there, but the anal vein is the last vein of the wing).

@Arthur I see the difference. However, I can't find in the text that this anal vein is a distinctive feature of all Hawk moths (though it very well might be). Do you have any better suggestions? AFAIK most Notodontidae and Noctuidae also have an anal vein reaching the outer margin.

@RHA while some elements of wing venation vary within Lepidoptera families, the number of anal veins reaching the wing margin in the fore wing isn't one of them (see here for another discussion of hawk moth wing venation -- sorry that there aren't pictures with this one; that same discussion lists other moth families which have the hind wings much smaller than the fore wings).

@Arthur I can't find anything about veins on that page.

@RHA sorry about that; I'd forgotten that not everyone is familiar with insect wing vein names.  It's in the fourth paragraph under the "Adults" header: the abbreviations R2 and R3 refer to the second and third branches  of the radius vein (the third major vein of an insect's wing after the costa -- at the leading margin -- and subcosta -- just after that); in the OP photo the forked vein we can see just past the fore wing apex is the last two branches of the radius: R4 and R5; the next five veins are the three branches of the media and two branches of the cubitus, all off the discal cell.


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Location of male and female reproductive organs in fern (prothallus)
I can't seem to find an authoritative answer to this anywhere else online.
Basically, my school text-book says the antheridium (male organ) is located on the lower surface of the fern prothallus and the archegonium (female organ) is located on the upper surface of the fern prothallus.
Another (somewhat unreliable) book mentions that both the antheridum and archegonium are located on the "ventral side". With regard to plants, I'm not quite sure what "ventral" is...is it the side that's in contact with the soil/substratum (i.e- the "lower" surface)?
Besides, which source is right? Or are they both wrong?

The acchegonium and antheridium are NOT found on the 'mature' plant, but on a gametophyte that grows from the spore. This is well illustrated in the "Petersons Field Guild to Ferns", https://www.amazon.com/Peterson-Field-Guide-Ferns-Northeastern/dp/0618394060 Click through the 'Look inside' pages and find the 'Life Cycle of a Fern' for details.


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Neuro-simulation tools
I know, this question is opinion-based, but where else should I ask it (or how could I ask it here without being flagged "opinon-based!")?
Which neuronal simulators - in the line of NEURON and GENESIS - are the "best", "mostly used", "mostly influential" today, not only in supercomputing, but also for small scale (personal) use?
The one I found best - even though designed for large scale applications - for my small scale (personal) requirements was nest, an explicit successor of NEURON. I have the impression, that nest is "better" for me than NEURON, in terms of usability, visualization, data exploration, ... but I don't know if there aren't even better neuro-simulation tools.
Would anyone mind giving his/her opinion?

I'd suggest asking questions like this that are a bit outside the normal SE rules in the Biology.SE chat. I'm most familiar with NEURON, though mostly in an educational rather than research context; I haven't used nest but if it is a successor to NEURON that's what I would recommend. One nice thing about NEURON is that there are so many examples/preexisting models to choose from, including some beautifully detailed volume reconstructions of real neurons; GENESIS may have the same, and I hope nest was able to preserve some of them.

I think it's a great question, and I hope it is not closed for being opinion-based. This is exactly the question I had years ago when starting on a project! Btw, you might also try the scientific computation SE as well.

I also think that this is a worthwhile, on-topic question, even if it is opinion-based.

I have only used NEURON and the DIY approach for small scale simulations.
You can have a look at this comparative table:

https://grey.colorado.edu/emergent/index.php/Comparison_of_Neural_Network_Simulators

which was last updated in 2014.
Except NEURON, GENESIS, and NEST, I have also heard positive comments about Brian.

Another option, maximal in terms of flexibility albeit also possibly effort, is to write your own. Of course, this presupposes some extra knowledge. However, I think coding your own gives a level of control that may be very difficult to attain with a library. Hence, it depends on the application.
(ModelDB has some examples of these.)
Of course, I don't recommend this for highly complicated cases (don't try to write your own code to solve SPDEs in volumetric meshes or something).
Using matlab or python (numpy & scipy) makes writing at least some of these models fairly straightforward, and both (especially the latter) have extraordinary scientific visualization capabilities. I have run neurosimulations like this on both my personal laptop and via hundreds of cores in clusters, so it is certainly viable in both cases.
Every model is approximation, and sometimes it is worth it to have better understanding and control of a simpler model than to have an enormously complicated one with huge numbers of different channels that may be hard to realistically choose (what is their spatial distribution and concentration? what are their parameters for the species of interest?). It depends on the phenomenon you want to simulate.

In any case, to speak of libraries, both NEST and NEURON seem like great choices. Personally, I've heard only of NEURON in any detail before.