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?

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.


Why do tails of some lizards break so easily? When I was younger once I have tried to catch a ground lizard by its tail but,
unfortunately the tail got broken and the lizard ran away.

Why did the lizard's tail get broken so easily while other animals have stronger tails?

It's a self-defense mechanism, the tail falls off during threatening situations, to which the reptile responds by excessively contracting the tail muscles. This process is known as "Autotomy", or "Self-Amputation". Other animals have got "stronger tails" simply because such self-defense mechanism hasn't been developed.
https://science.sciencemag.org/content/20/500/149.2
Check this link for more in depth information!


How do we know if a neuron is inhibitory or excitatory? The textbook examples for an excitatory neurotransmitter is Glutamate, and for an inhibitory neurotransmitter it is GABA.

In my naive understanding, a neuron was inhibitory or excitatory depending on the neurotransmitter it releases onto its postsynaptic partners.

According to this thread, however, a neurotransmitter is not per se excitatory or inhibitory, but this property depends on the postsynaptic receptor it is acting on.

Now this property seems independent of the presynaptic cell - hence, how can we classify the presynaptic cell of being either inhibitory or excitatory (when that is a property of the postsynaptic receptors, which can be either)?

Besides, given that we a huge number of neurons and their connections in each $mm^3$, how can we be sure that the presynaptic's cells action are not mediated by other cells, and the observed inhibition/excitation is not rather a network effect?

In my naive understanding, a neuron was inhibitory or excitatory depending on the neurotransmitter it releases onto its postsynaptic partners.

This is mostly correct. What remains a question is what makes a given neurotransmitter inhibitory or excitatory. To some extent, that depends on the post-synaptic receptors, but also depends on other conditions: one case mentioned in the linked Q&A that I'll repeat is that GABA is actually excitatory at some times, including during development (and the same thing can happen in certain causes of epilepsy). In that case, the reason is because GABA-A receptors are chloride channels, so the reversal potential for chloride is what matters. If the reversal potential for chloride is more hyperpolarized than threshold, GABA-A is an inhibitory receptor; if the reversal potential for chloride is more depolarized than threshold, GABA-A is an excitatory receptor. Chloride ion concentrations are different during certain stages of development so the role of GABA changes (in development it seems like it is important for development of eventually inhibitory circuitry).

I digress a bit, but I think you've really already encountered all you need to know: labels like "excitatory" and "inhibitory" for a neurotransmitter itself are generalizations that satisfy human preferences for heuristics. It's convenient to talk about GABA as an inhibitory neurotransmitter, because in most cases the major systemic effect of GABA is inhibition. Same with glutamate in the direction of excitation.

Most of the inhibition caused by glutamate is the presynaptic inhibition type discussed in a previous Q&A; that is, it is suppressing the release of glutamate itself. In that sense, glutamatergic inhibition is only as effective as glutamatergic excitation is: the net effect of glutamate will always be excitatory in that system.

Therefore, it is straightforward to consider GABAergic and glutamatergic cells inhibitory and excitatory, respectively.

  how can we be sure that the presynaptic's cells action are not mediated by other cells, and the observed inhibition/excitation is not rather a network effect?

The principle way is by pairwise recordings: you record from the presynaptic and postsynaptic cell at the same time, activate the presynaptic cell, and measure the voltage in the postsynaptic cell. These sorts of pairwise recordings are a common tool in neuroscience.

Cancedda, L., Fiumelli, H., Chen, K., & Poo, M. M. (2007). Excitatory GABA action is essential for morphological maturation of cortical neurons in vivo. Journal of Neuroscience, 27(19), 5224-5235.

Owens, D. F., Boyce, L. H., Davis, M. B., & Kriegstein, A. R. (1996). Excitatory GABA responses in embryonic and neonatal cortical slices demonstrated by gramicidin perforated-patch recordings and calcium imaging. Journal of Neuroscience, 16(20), 6414-6423.

Thomson, A. M., & Deuchars, J. (1997). Synaptic interactions in neocortical local circuits: dual intracellular recordings in vitro. Cerebral cortex (New York, NY: 1991), 7(6), 510-522.


What type of tree is this? (Coyote Hills) I found this in Coyote Hills, Los Angeles, USA. Please provide the common name.

I guess it is Schinus molle (Peruvian pepper)


What causes fingerprints to form and why is the pattern formed unique? I've found research that suggests that the reason we develop fingerprints is because they aid us with feeling surfaces (Scheibert, et al. 2008) and not to increase friction  and help with the gripping of smooth objects (Warman and Ennos 2009).

One thing I am still curious about is at what stage of growth the pattern is formed and why a unique pattern is created in the fingerprint of each person (including identical twins). I assume it has something to do with the mechanism by which the patterns form, but I couldn't find any detailed research into this. Any insight would be very welcome.

I would say genetic diversity is the primary reason which results in other reasons that you are looking for. At the lowest level, random crossing over at prophase I, random separation of homologous chromosomes at anaphase I, random separation of sister chromatids at anaphase II, and random fertilization: one sperm fertilizes one egg randomly.

The skin is developed from ectoderm so need to look at the formation of embryonic disc and specifically to the genesis of germ layers: ectoderm.

However, I would stick to the primary reasons, since it is extremely difficult to visualize the given formation - actually we do not have resources for it at the moment.

Very good question the last part. I have an intuition that skin develops randomly because of the above reasons. You would also need a lot of memory to make identical skins for twins! It has not been useful to have identical fingerprints between two people so evolution has not resulted into it.

Feeling surfaces and gripping are movements - not much space taken things, in contrast to the memory needed in storing the exact surfaces of skin from one generation to another. - Learning is a way to save resources here and it is a lot more efficient and than storing static information to species from one generation to another.


Why is the relative expression in qPCR so low? When analyzing different mutations through qPCR I found the $2^{-\Delta\Delta ct}$ value for each mutation. All the mutation have similar values compared to the wild type gene, however one of the mutation has an extremely $2^{-\Delta\Delta ct}$ value. Having $1$ for the wilde type, and an average of $0.9$ for some mutant genes, the exceptional case has a $0.05$ value.

I think one could argue that this mutation deletes a sequence from the wild type gene, but I believe other things can be suggested from this.

It may be a particular mutation that affects expression altogether. Through qPCR you're able to tell the relative difference in mRNA levels of a particular gene between, say, a WT and a mutant. It may be that this particular mutation damages some regulatory sequence within the body of a gene (e.g. a downstream promoter element) or some regulatory sequence upstream. To me, this suggests that you're dealing with such a case here. Anyways, you'd need more data to tell for sure. You should have the mutation mapped, if you haven't already and check if the primers you used were  okay. This mutation clearly hampers expression, as long as everything was okay with the procedure.


What does fail-safe mean in transmission at electrical synapses? I'm reading a book named Neuroscience:Exploring the Brain recently. And in the chapter about synaptic transmission, it says "Transmission at electrical synapses is very fast and, if the synapse is large, fail-safe." So what does fail-safe mean? And why is that transmission fail-safe when the synapse is large?
And when is comes to EPSP, it also mentions that "The neuromuscular junction has evolved to be fail-safe; it needs to work every time, and the best way to ensure this is to generate an EPSP of a huge size." I don't understand the meaning of the word and the whole sentence.

To understand what failure means in this context, we need to know a bit about how signals are communicated from one neuron to another.

Types of signals

First of all, it's important to know that synaptic signaling (communication between neurons) comes in two flavors: chemical and electrical.  The signaling is done at the interface between two neurons, known as the synapse.  There are generally dozens to hundreds of synapses between two connected neurons.  At chemical synapses, a chemical (the neurotransmitter) is released into the space between the pre-synaptic site on the axon and the post-synaptic site on the dendrite (or soma).  At electrical synapses, no chemicals are released.  Instead, porous proteins called “gap junction channels” bridge the space between the cell membranes of two neurons and create pores that allow electrical current to pass directly from one neuron to the other.

Signaling is probabilistic

Second, it's important to appreciate that neurotransmission is probabilistic, rather than deterministic.  That just means there’s a chance that signaling from an upstream neuron might fail to evoke a response in a downstream neuron.  There are several reasons why transmission is not 100% efficient, at both the pre-synaptic and post-synaptic ends.

Some of these reasons have to do with spontaneous opening and closing of channels in the membrane.  When researchers examine electrical currents flowing through single ion channel proteins they find that each channel randomly flips between open and closed states.  This is caused by molecular-scale fluctuations in the protein's shape that cause it to either block or allow the passage of electrical current (or ions).

In addition, random fluctuations in how well electrical current is able to be integrated by the downstream neuron add to the variability in signaling that makes responses probabilistic. You probably already know that "response" of a neuron refers to the firing of action potentials. And you probably also know that action potentials are generated when the membrane of a neuron becomes sufficiently depolarized - the result of a process known as synaptic integration.  A simple view of synaptic integration is the summing together of all electrical currents flowing across the membrane from different synapses in a short window of time.  If this current integrates to a total greater than some value (the firing threshold) the neuron fires, otherwise it does not.  What some may not realize, though, is that this process isn't perfect - current can leak out of the cell, other neurons can "siphon off" current, and receptor proteins in the downstream neuron can become inactive and stop contributing to the overall current flux.

All of these factors conspire together to make the signaling process probabilistic. Because there's always less than a 100% probability that signaling from an upstream neuron will sufficiently excite a downstream neuron, there will be occasions where a downstream neuron fails to fire.

So taking these things into account, we can define the following:

SUCCESS = Neuron A fires -> causes Neuron B to fire
FAILURE = Neuron A fires -> Neuron B does not fire

An example

If a synapse has 100 channels, and each channel has a 50% chance of being open at any moment, then we expect that, on average, 50 channels will be open at any given time.  If each channel can allow 1pA of current to pass through, this synapse will transmit on average 50pA of current from Neuron A to Neuron B.  Let's say 25pA is needed to bring Neuron B to threshold and cause it to fire.  Then this synapse will typically transmit more than enough current to evoke a response in Neuron B.

But here's the catch.  Because the inactivation of each channel is spontaneous, sometimes there will be more than 50 channels open, and sometimes less than 50 - just by chance.  On some rare occasions, fewer than 25 channels will be open, and if Neuron A fires at one of these crucial moments, our 100 channel synapse will transmit less than 25pA, and fail to bring Neuron B to threshold.  This is how an electrical synapse "failure" occurs. You can imagine how, evolutionarily, this might be a bad thing if that failure to fire Neuron B occurs at a crucial moment when the muscle under control of Neuron B is needed to jump out of a predator's reach.

This leads us to the question:
Given these definitions, how would we increase the chance of success, and correspondingly decrease the chance of failure?

Scaling up

Well, probability makes things a numbers game, and here's where size comes into play.  One way we could make sure that Neuron A has a really good chance of firing Neuron B is to mitigate the risk from spontaneous channel inactivation.  We could do this by simply scaling up the synapse - making it larger and adding more channels.  If we had 200 synapses, rather than 100, and they all still had a 50% chance of being closed at a given moment, then the chance becomes incredibly remote that, at a given moment, fewer than 25 channels (the number needed to fire Neuron B) are open and able to transmit signal.  This is what's meant by being made fail-safe.

It's easy to see that another means to the same end is to scale up the corresponding response in Neuron B - the EPSP - as observed at the neuromuscular junction.  By scaling up the strength of the response, it becomes less likely that random, uncontrollable influences on the cell (or muscle) would cause a failure to fire.

Hopefully, now you can see how neurons may fail to signal, and why scaling things up can, in general, make a synapse more fail-safe.


Can a plate with incompletely filled LB agar be used? I am falling short of LB agar plates and I have a plate with less LB agar poured. I meant, the plate is not fully filled with the agar (it was the last plate I poured the medium into). Some part of plate is empty. Does this cause any contamination problems or moisture retention? Is it okay if I use this to streak a 5 cm line?

It won't be a problem other than that the surface would be uneven. Seal the plate with parafilm when not using to avoid moisture from accumulating inside. When you pour plates then swirl the plate gently so that the molten agar distributes evenly throughout the plate. The agar will be thin though, and you would have to streak gently so as not to cut the agar; you can add 0.5 % of normal agar-agar to make it a little dense.

Or else use  smaller plates (2 inch) if you have them in your lab.


What is the relationship between migraines and histamine? A family member suffers from migraines so I have been reading a little around the subject.

There seem to be any number of "triggers", but I have seen mention several times of the role of histamine in migraine activation as an active area of research. The suggestion is that high histamine levels in the body can cause migraines.

Is there solid evidence that histamine can trigger migraines?  How does this mechanism operate?

Yes, this is true.
Histamine is thought to induce the enzyme Nitric Oxide (NO) Synthase.  NO is then available to act locally on the vasculature as a vasodilator.
NO binds to guanylyl cyclase in vascular smooth muscle cells, which leads to the production of cyclic GMP, which in turn forms phosphorylated protein kinase G. PKG phosphorylates Ca2+ channels, slowing the influx of calcium into the cell, which leads to smooth muscle relaxation, and vasodilation, which leads to migraine.
The only silver lining is that there is a check in place: with the binding of histamine to H3 receptors on c-fibers in the central nervous system, feedback inhibition prevents the further release of histamine from these sites.
References:

Akerman S, Williamson DJ, Kaube H, Goadsby PJ. (2002).  The role of histamine in dural vessel dilation.  Brain Res. 956(1):96-102.
Gupta, S., Nahas, S.J.,Peterlin, B.L. (2011) Chemical Mediators of Migraine:
Preclinical and Clinical Observations.  Headache: The Journal of Head and Face Pain, 51(6): 1029–1045.


Zoology - Help identify the kind of spider Yesterday, I bought a banana tree (Musa Basjoo) from a local supermarket.
Today, I noticed a hive of small spiders on the tree.
I do not know where they came from, so I am curious to identify these small creatures.
I am living in Flossenbürg, Bavaria, Germany.

Can someone help me identify the kind of spiders that are depicted on the photos?

A picture of the tree, it is still in front of my house door, planted in a pot:

A near shot of the spiders that are "dwelling" on the tree:

Not too sure but it seems like the european garden spider- Araenus diadematus

[ Image source ]


Is the squid giant axon the fastest conducting unmyelinated axon known? The conduction velocity of the squid giant axon can reach 30 m/s. Is there any known example of an even faster conducting unmyelinated axons?

The conductance velocity in the unmyelinated axon has been calculated and measured to be proportional to the square root of the axon diameter (see for example: Rushton, 1951). Since the giant axon is, well, giant, it conducts much faster than others. AFAIK, all other large neurons studied are myelinated. Maybe try to find bigger squids! ;)


Insect with long neck—what is it? I found this insect in Fish Haven, Idaho (right next to Bear Lake) in June and think it’s absolutely fascinating:

If you can’t tell from the picture, it’s a few centimeters in length—very thin with a pair of transparent wings that extend straight backwards past the end of the abdomen. The thorax is brown, and past the point where the wings connect it is long and neck-like, leading to a black head with two long antennae. Can anyone identify this insect?

That appears to be a species of snakefly and the lack of a long needle-like ovipositor indicates that this specimen is a male.

The "kite" rather than rectangular head shape suggests it is in the Raphidiidae.

From the location I think it could be in the genus Agulla and might be the Idaho Snakefly (Agulla adnixa), but I don't know if that is the only species from this group in that area.

Reference image (Copyright © 2007 by Hartmut Wisch) from BugGuide.net:


Identifying very tiny worm i couldn't take a picture because i get rid from it as soon as posible. Because i thought maybe it was a bad parasite.

But i draw a picture of it at my computer. But my picture not very accurate because it was very tiny to see what it actually look like. and i cant remember all of the characteristics of it.

It is very tiny about 5 mm in length. and maybe almost 0.1 mm thick. I assume that yellow thing is head, because of movement directions is towards that way. To move, he elongates its own body then holds to surface with its own head, then let free its other ends grasp from the surface simultaneously shrinks to shorter length maybe half of its elongated length. than repeats whole process.

It was shrinks and elongates to move

it was moving like its got very soft body. and it was becoming significantly thinner when elongates.

Sometimes looks like checking surrounding surface with his head. Seem like it tries to navigate.

finally I must describe how my picture could inaccurate: it was very tiny i cant see his body parts exactly. i guess i see a tiny structures appears like his 2 pair back leg and 1 structure ball like thing attached to end. But this structures possible thickness are micrometers so i also thought that structures could be attached dust particles. And i also saw structures like this at the front end, but it was so tiny, i cant even drew because i see just barely but cant figured what was it like.

only im sure about its head and white-ish neck.

it is elongated at the picture.

So picture is representing what i see. but not %100 accurate. due to reasons i described.

i hope my questions description is enough and isn't improper.

Was it an inchworm? It fits the description, as well as the 2nd picture.


How do bees help flowering trees survive? I have often heard a vague claim that bees help flowering tree populations survive.
As far as I know, bees take nectar and pollen concentrations from the flowers of flowering trees and use at least the nectar as a food source, but they don't take seeds out of these trees, so it's unclear to me how they help these trees survive in that regard.

Given that bees don't take seeds of flowering trees (and drop some when they fly) How do bees help flowering trees survive?
How does the taking of nectar and pollen away from flowering trees make bees symbiotically help such tree populations to survive and endeavor?

One of the goals of every living organism (including plants), thus it seems, is to create offspring for the next generation. This is the way plants (angiosperms) have sex.

That said; I personally define pollination as:

  The act of transferring pollen grains from the male anther of a flower
  to the female stigma.

It should be noted that not only Bees play a very important role in pollination, but also other insects like wasps, beetles, mosquitoes etc.

When a bee sits on the flowers to collect nectar, its feet pick up pollen grains ( the powdery stuff) from the anthers and transfer it to the female stigma (which is sticky to hold the pollens).

Michigan State University:

  When a bee lands on a flower, the hairs all over the bees' body attract pollen grains through electrostatic forces. Stiff hairs on their legs enable them to groom the pollen into specialized brushes or pockets on their legs or body, and then carry it back to their nest. Individual bees tend to focus on one kind of flower at a time, which means it is more likely that pollen from one flower will be transferred to another flower of the same species by a particular bee.

Then the pollen grain makes its way into the ovary of the flower through the long stalk (style) and fertilizes the egg. Then the flower matures to for a fruit and the ovules become it's seeds.
It's a symbiotic relationship where the plant provides food and the bees pollinate them in turn.
Also, certain bright colouration of flowers and their sweet smell attract more insects.

A declining population of pollinating insects signal the decline of the whole ecosystem including plants and trees.
Entomologists keep a check on various insect populations. They have found a decline in the population of bees world wide! This is an alarming situation. This will cause huge damage to fruit industries including kiwifruit, watermelon, squash and many others. It's time we take the environmental issues seriously.The reports aren't vague!

Penn State College of Agricultural Science:

  Historically, managed honey bee populations in the US and Europe have been monitored due to their vital role in providing pollination services in agricultural systems.  Several studies indicate that American and European beekeepers are suffering large annual losses.  In the US, beekeepers have lost ~30% of their colonies every year since 2006, with total annual losses sometimes reaching as high as 42%

Edit

Citations:

https://en.m.wikipedia.org/wiki/Pollinator#Honey_bees

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

A brochure from FAO on importance of bees as pollinators :
http://www.fao.org/3/I9527EN/i9527en.PDF

Penn State College of Agricultural Science on declining population of pollinators :
https://ento.psu.edu/pollinators/resources-and-outreach/globally-pollinators-are-in-decline

Wikipedia on the same issue:
https://en.m.wikipedia.org/wiki/Pollinator_decline


Why isn't a virus "alive"? The recent news about a new supermassive virus being discovered got me thinking about how we define viruses as non-living organisms whilst they are bigger than bacteria, and much more complex than we first gave them credit for.

What biological differences between viruses and cellular organisms have made viruses be deemed non-living?

If this is a topic that really interests you, I'd suggest searching for papers/reviews/opinions written by Didier Raoult.  Raoult is one of the original discoverers of the massive Mimivirus and his work will lead you to some truly fascinating discussions that I couldn't hope to reproduce here.

The main argument for why viruses aren't living is basically what has been said already.  Viruses are obligate parasites, and while plenty of parasites are indeed living what sets viruses apart is that they always rely on the host for the machinery with which to replicate.  A parasitic worm may need the host to survive, using the host as a source for energy, but the worm produces and synthesizes its own proteins using its own ribosomes and associated complexes.

That's basically what it boils down to.  No ribosomes?  Not living.   One advantage of this definition, for example, is that it is a positive selection (everyone "alive" has got ribosomes) which eliminates things like mitochondria that are sort of near the boundary of other definitions.  There are examples on either side of something that breaks every other rule but not this one.  Another common rule is metabolism and while that suffices for most cases some living parasites have lost metabolic activity, relying on their host for energy.

However (and this is the really interesting part) even the ribosome definition is a bit shaky, especially as viruses have been found encoding things like their own tRNAs.  Here are a few points to think about:

We have ribosome encoding organisms (REOs), so why can't we define viruses as capsid encoding organisms (CEOs)?
Comparing viruses to a living organism such as a human is absurd, given the massive differences in complexity.  A virus, really, is just a vehicle or genetic material, and would be more rightly compared to a sperm cell.  Is a sperm cell alive, or is it a package for genetic material that is capable of life once it has infected/fertilized another cell?
The really large DNA viruses often create cytoplasmic features called virus factories.  These look an awful lot like a nucleus.  What is a nucleus anyway?  Maybe it's just a very successful DNA virus that never left.
Viruses can get viruses.

I'll wind down here, but suffice to say that while our current definition may have sufficed for a while, and still does, it is no longer quite solid.  In particular, there is a theory alluded to above that eukaryotic life itself actually formed because of viruses.  I can expand on this if you like, but here are some great sources:

Boyer, M., Yutin, N., Pagnier, I., et al.  2009.  Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms.  PNAS.  106(51):21848-21853 (http://dx.doi.org/10.1073/pnas.0911354106)

Claverie, JM.  Viruses take center stage in cellular evolution.  2006.  Genome Biology.  7:110. (http://dx.doi.org/10.1186/gb-2006-7-6-110)

Ogata, H., Ray, J., Toyoda, K., et al.  2011.  Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment.  The ISME Journal.  5:1143-1151 (http://dx.doi.org/10.1038/ismej.2010.210)

Raoult, D. and Forterre, P.  2008.  Redefining viruses: lessons from Mimivirus.  Nature Reviews Microbiology. 6:315-319. (http://dx.doi.org/10.1038/nrmicro1858)

Scola, B., Desnues, C., Pagnier, I., et al.  The virophage as a unique parasite of the giant mimivirus.  2008.  Nature.  455:100-104 (http://dx.doi.org/10.1038/nature07218)


Why and where do red blood cells die? Textbooks commonly state that red blood cells are removed by the liver and spleen. Do those organs destroy the red blood cells within capillaries that course through those organs or are they transported into the liver/spleen cells to be broken down into their constituents? What causes them to be destroyed/removed from the circulation?

To take the easiest bit first: Red blood cells are destroyed because lacking a nucleus, they aren't quite as powerful as other cells when it comes to self-repair and longevity.

As for where; it really is all over the body. They are swallowed up (literally) by macrophages lining the blood vessels, which are particularly concentrated in the liver, spleen and bone marrow, but present everywhere.

As they age, they deform, and the macrophages are capable of recognising this deformation and reacting to it (by eating the red blood cells).

When the macrophages have eaten and destroyed the red blood cells, the nutrients they contain are returned to the blood plasma, and captured in the bone marrow for production of new blood cells.

(This pattern is common in a lot of systems, by the way: Even though the liver is the primary organ to break down toxins, for instance, most cells in the body has some limited capability for doing so; this is true of many functions.)

Ref:

http://bril2002.narod.ru/bllod56.html
https://en.wikipedia.org/wiki/Drug_metabolism#Sites


Why is the hippocampus considered to be a cortical structure but not the amygdala? I'm having some trouble understanding the anatomical differences that classify the hippocampus as a cortical structure but not the amygdala. I have included the screenshot of a diagram from Gray's Clinical Neuroanatomy.

Medial aspect of the left cerebral hemisphere demonstrating some limbic structures (yellow). The anterior nuclear group of the thalamus is coloured orange, and the rest of the thalamus is magenta. The approximate position of the brain stem is outlined in a heavy interrupted line.

You can't distinguish cortical from deep structures from a picture like the one you reference in Gray's Clinical Neuroanatomy. The hippocampus is a cortical structure because its cell bodies are in the outer layers of the cerebrum. The amygdala is a deep structure because its cell bodies are in nuclei. I'm not sure if your textbook has stained sections, but if it does, that should help clarify the difference between the two structures.

In this sagittal section you can see both. Notice the hippocampus (at both ends) follows the bumps and grooves of the cortex where the amygdala is a circular/almond shaped cluster of cells.


A timeline of the odds for survival for fertilized eggs and fetuses I'm looking for data to build a timeline of the odds for survival of a fertilized egg, i.e.,

What are the odds it'll last a week?
What are the odds it'll last a month?
2 months?
(and so on until)
What are the odds of it being born?

I am interested in the odds with the usual level of care in an industrialized nation (and a mother that is not trying to abort the fetus).

here I found an answer. Not sure how accurate is is, though.

Data seems to be from the US

Here is a rewrite of parts of that article:

266 days before birth, all we have is a fertilized egg.  (~33% chance of living birth).
The odds are calculated using data from in-vitro fertilization, and the next stage is 66%.
In in-vitro, some 50% of the eggs cannot fix to the uterine wall
262 days before birth, the egg has implanted (~66% chance of living birth)
After implantation, there is still a decent chance that the embryo will be aborted (and maybe the woman will not even know that she was pregnant).
Half of the embryos that die from here on will die because of chromosome abnormalities.
241 days before birth (~88%)
178 days before birth, entering the second trimester (~97%)
At this stage, problems are more likely to stem from the mother, not the fetus' genome. Problems with the cervix, the uterus or the placenta are (some ?) likely causes of death.
89 days before birth, entering the third trimester (~99%)
At this stage, doctors will consider the fetus a patient, and treat it if needed.


By selecting sex cells after meiosis, would it be possible to create two offspring with inverse parental DNA of one another? Would it theoretically be possible to select two sex cells after a male meiosis (filtering out the two where crossover had taken place) and combine each with two sex from a female meiosis (imagining they were all egg cells, even though only one would be) to create offspring with inverse inherited parental DNA of one another?
For example: If the mother's DNA is AB and father's is CD then the offspring could have AC and BD - inherited from both parents but completely different from one another.

Theoretically? Yes. Very theoretically possible.
In practice? It's difficult to isolate the exact daughter cells (sperm) from the same meiotic event, have these cells complete maturation, and only then have them fertilize an egg. Normally you need quite a lot of sperm cells even with in vitro fertilization, but also in principle all you need would be a single sperm cell to make a zygote!
To address some misconception: when you say "inherited from both parents but completely different", that applies also for regular sex cells and fertilized eggs. You don't need to fish for the precise 2 daughter cells following meiosis to get this outcome. Mitosis produces 2 genetic copies, while meiosis in humans produces 4 unique daughter cells. All individuals, as diploid as we are as humans, are products of genomes that have been very well shuffled (recombined).
Reality: the real-life reasons to perform such a procedure would be taken as very dubious, so I don't think realistically anyone would perform this. But in the designer baby era of the future, who knows!


Why is amylose insoluble in water? In a handout the following is stated:

  Amylose is insoluble in water, therefore a good storage compound e.g. in stroma of chloroplasts

This is with regard to the chemical structure of the molecule.

However it has left me wondering, what is it intrinsically about the structure of a molecule that makes it soluble/insoluble in water?

My thoughts at this stage are perhaps to do with whether the molecule is hydrophobic, and if that is the case - how is amylose hydrophobic?

The availibity of -OH groups for hydrogen bonding with polar water molecules is reduced in amylose due to its coiled nature (resulting in part by H-bonds between the glucose monomers).  Amylopectin is even less soluble due to the additional 1-6 glycosidic bonds on the branch chains, further reducing its H bonding potential and therefore reducing solubility in water.


How do transplanted stem cells find their way to bone marrow? Miraculously, transplanted stem cells find their way to the bone marrow missing the stem cells. How do they achieve this?

The transplantation is an equivalent of a process that naturally occurs in human body, homing of the hematopoietic stem cells.

Immature hematopoietic stem cells have the ability to pass the bone marrow barrier, and therefore is able to migrate between bones and other organs within an individual. (e.g. thymus, which is how it can produce T cells.) Williams et al. believe that the process, homing, is a complex interaction and is similar to the migration of leukocytes to inflammatory sites. 1

Peripheral stem cell transplantation makes use of this ability. The donor first will be administered with certain drugs to proliferate stem cells in bone marrow and hereby raising the concretion of hematopoietic stem cells in blood. Those stem cells in blood then will be collected and transfused into the recipient. Eventually those cells will find their way home.


Why do parasites sometimes kill their hosts? It's bothered me for a while now. I understand why a parasitoid would do this, as it only temporarily requires the host, and that not all parasites kill their hosts.

There seems to be no evolutionary advantage in killing a host, because the parasite relies on the host for resources. Yet some organisms, usually microscopic pathogens, seem to fatally damage the host with no immediate benefit to themselves. Why is this?

I know this is asking for a broad soft answer, but I don't want the question to get bogged down by a specific species, although bonus points for using examples.

I can think of several (non-exclusive and probably non-exhaustive) hypotheses:

Maladaptive. It is maladaptive. Maybe because it is a virus coming from another species (e.g. SIV and HIV) or because it is not adapted to our modern lifespan.
Benefit of the host immune system to the parasite. Some parasites might benefit from host immune defence (e.g. sneezing helps bacteria to spread) and death is a consequence of the selection for increasing disease symptoms to the host.
Pathogen's and host's fate. The pathogen's fate is not linked to the host's fate. This is especially true if the pathogens spread well (easily jump from one host to another) I guess or for parasitoïd because the pathogen leaves its parasitic life after the death of its single host.
intra- and inter-host selection. Among hosts, there might have a selection for reducing resource consumptions and therefore for decreasing the probability for the host to die. But within a host (among individuals of a parasite population or even among parasite species), it is a prisoner's dilemma (tragedy of the commons). The more you invest in foraging, the more competitive you are. This might not be adaptative at the population level but it is at the individual level. We might think of this prisoner's dilemma happening among individuals of a single parasite species or among several parasite species. You may want to have a look at the work of Martin Nowak on the subject incl. Consider for example his book; Evolutionary Dynamics.
Consequence of harming on trade-offs. Harming an individual will cause him not to spend energy into reproduction in order that more energy is available for the pathogen use. Moreover, by causing symptoms, the infected individual will be sexually less attractive and will again have less opportunity to spend energy into reproduction.
The pathogen does not mean much harm. When fighting pathogens, many of the symptoms we experience (such as fever typically) are actually caused by the immune system and not the pathogen itself. A maladaptive overreaction of the immune system can cause our death.

The book Why we get sick by Randolph Nesse and George Williams, will probably interest you.


What is ApoCas9 in the CRISPR-Cas9 system? I am currently reading an article about a particular assay of Cas9 nucleases. In one of the experiments, they have used ApoCas9 (Apo variants of other CRISPR nucleases) as some sort of control.

But the whole article they have not defined ApoCas9? I did check online of definition and activity of ApoCas9, but came across without any fruitful results.

A universal method for sensitive and cell-free
detection of CRISPR-associated nucleases

In general, "apo" is used to indicate an apoenzyme — that is the protein part of an enzyme without essential cofactor(s).

This is actually defined in the Experimental section of the paper:

  Cas9/Cpf1 without gRNA (ApoCas9/Cpf1)

So, in this case ApoCas9 is Cas9 endonuclease that is not bound to a guide RNA.


Could the protein dystrophin be artificially synthesised? Could the protein dystrophin be artificially synthesised and if so could patients with DMD (Duchenne Muscular Dystrophy) benefit from it?

//Now I don't have much scientific background other than a high school biology qualification

I met someone the other day the same age as me who suffers from DMD, so I did some research and curiosity led to this question.

Sorry if I used the wrong tags or/and this question isn't allowed. \

Great question.

Yes, it is almost certainly possible to artificially synthesize just about any protein. There can be difficulties with certain proteins, but these are more engineering problems rather than true limits to artificial synthesis.

The problem is getting the protein where it needs to be to be functional!

A great comparison is insulin. Insulin is an important regulatory protein that floats around in the bloodstream. That makes insulin therapy a relatively straightforward solution to a problem of not enough insulin: all you have to do is make or isolate some insulin and inject it into the bloodstream.

Dystrophin, however, is a structural protein that acts inside cells. Proteins are really big, and they can't be simply taken up by cells. There's no mechanism to get an arbitrary protein inside: any proteins that can be taken up by cells need to do so via some specialized mechanism.

If you wanted to replace a defective allele for dystrophin, then, the most feasible approach would be gene therapy: getting a patient's own cells to produce a functional copy of the protein. Efforts to entirely or partially replace dystrophin via gene therapy are a current area of research, but there are still many challenges to gene therapy approaches in general.

References

Harper, S. Q., Hauser, M. A., DelloRusso, C., Duan, D., Crawford, R. W., Phelps, S. F., ... & Chamberlain, J. S. (2002). Modular flexibility of dystrophin: implications for gene therapy of Duchenne muscular dystrophy. Nature medicine, 8(3), 253.

McGreevy, J. W., Hakim, C. H., McIntosh, M. A., & Duan, D. (2015). Animal models of Duchenne muscular dystrophy: from basic mechanisms to gene therapy. Disease models & mechanisms, 8(3), 195-213.

Pichavant, C., Aartsma-Rus, A., Clemens, P. R., Davies, K. E., Dickson, G., Takeda, S. I., ... & Tremblay, J. P. (2011). Current status of pharmaceutical and genetic therapeutic approaches to treat DMD. Molecular Therapy, 19(5), 830-840.

Verhaart, I. E., & Aartsma-Rus, A. (2012). Gene therapy for Duchenne muscular dystrophy. Current opinion in neurology, 25(5), 588-596.


Primer Dimer / Hairpin Algorithms What are the algorithms / methods in use for the calculation of primer dimers and hairpins?

As an example, IDT's OligoAnalyzer tool will generate these analysis given particular sequences.

The homo-dimer analysis seems to me to just be a sliding scan of two sequences across each other. I assume this doesn't take into account possible hairpin issues? or are such structures less likely compared to the myriad of other more common problems.  In addition, how are the ΔG values calculated given a particular dimerization pattern?

It is important visualize more faces to design primer or oligo and PCR experiments:

- calculate thermodynamic parameters of DNA Hybridization (Oligo/Template)

compute hairpin-loop, dimer, bases penality and melting temperature about primer or pair primer
calculate statistics about melting temperature with the change in composition and mix PCR concentration

with google you could find more tools but you must choose a tool of a sequencing team.
almost all tools use mfold algorithm, it's simple and effective:

M. Zuker, D. H. Mathews & D. H. Turner. Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide In A Biochemistry and Biotechnology, 11-43, J. Barciszewski and B. F. C. Clark, eds. , NATO ASI Series, Kluwer Academic Publishers, Dordrecht, NL, 1999.

I worked in a sequencing team and there was a programmer. he developed a fantastic tools. he is a little english, but he could support you: http://promix.cribi.unipd.it/cgi-bin/promix/melting/melting_main.exe


What does "~mitochondrial DNA ~bp linear DNA" means? I'm surfing NCBI website -Nucleotide- to find some examples of real DNA sequences to use in my small homework project.
My question is related to the title of a DNA sequence below:

Sus scrofa mitochondrial DNA, D-loop region, isolate: Europeanwild boar 3
1,045 bp linear DNA

I thought a mitochondrial DNA is different than a linear/nuclear DNA, especially that a mitochondrial DNA is circular while a linear/nuclear DNA is linear. So what does the above title actually means (in simple terms)? Is it still linear or not?

Well, Mitochondrial DNA CAN be linear (in some organism), see the wikipedia page on this

  In most multicellular organisms, the mtDNA - or mitogenome - is
  organized as a circular, covalently closed, double-stranded DNA. But
  in many unicellular (e.g. the ciliate Tetrahymena or the green alga
  Chlamydomonas reinhardtii) and in rare cases also in multicellular
  organisms (e.g. in some species of Cnidaria) the mtDNA is found as
  linearly organized DNA. Most of these linear mtDNAs possess telomerase
  independent telomeres (i.e. the ends of the linear DNA) with different
  modes of replication, which have made them interesting objects of
  research, as many of these unicellular organisms with linear mtDNA are
  known pathogens.[19]

  For human mitochondrial DNA (and probably for that of metazoans in
  general), 100-10,000 separate copies of mtDNA are usually present per
  cell (egg and sperm cells are exceptions). In mammals, each
  double-stranded circular mtDNA molecule consists of 15,000-17,000[20]
  base pairs. The two strands of mtDNA are differentiated by their
  nucleotide content, with a guanine-rich strand referred to as the
  heavy strand (or H-strand) and a cytosine-rich strand referred to as
  the light strand (or L-strand). The heavy strand encodes 28 genes, and
  the light strand encodes 9 genes for a total of 37 genes. Of the 37
  genes, 13 are for proteins (polypeptides), 22 are for transfer RNA
  (tRNA) and two are for the small and large subunits of ribosomal RNA
  (rRNA). This pattern is also seen among most metazoans, although in
  some cases one or more of the 37 genes is absent and the mtDNA size
  range is greater. Even greater variation in mtDNA gene content and
  size exists among fungi and plants, although there appears to be a
  core subset of genes that are present in all eukaryotes (except for
  the few that have no mitochondria at all). Some plant species have
  enormous mtDNAs (as many as 2,500,000 base pairs per mtDNA molecule)
  but, surprisingly, even those huge mtDNAs contain the same number and
  kinds of genes as related plants with much smaller mtDNAs.[21]

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

In the case of your sequence, it only means that it has been entered in NCBI as a linear piece of DNA (it is usually the case when you sequence only a piece of a circular DNA for example)
It does not mean that within the organism it is linear !

I hope this answers your question !


Using nanodrop for analysing biological samples other than nucleotides I am a 3rd timer postdoctoral fellow with some experience in molecular biology and biochemistry, but major skills in Zoology and Natural History. I am studying some natural extracts, and isolating compounds.

Some biological samples come in limited amounts (e.g. invertebrate haemolymph), hampering analytical methods that rely on larger amounts. For instance, establishing UV-Vis spectra of extracts is a usual non-destructive method for approaching unknown samples and estimating general parameters, done with a spectrophotometer.

The microvolume-scaled spectrophotometer system popularly known as 'Nanodrop' has been around labs since almost two decades now. Its use has been usually limited to fast purity & concentration estimations for DNA & RNA in molecular biology labs.

I am considering using the nanodrop to estimate parameter of other biological and chemical samples. The manual says most commonly used solvents are compatible with the system. I have however yet found no-one else who has tried using Nanodrop for different applications.

Please, anyone here who has experimented using a Nanodrop system with other biological samples and extracts could comment on the experience?

The Nanodrop is a generic UV-visible spectrophotometer. According to the manufacturer, the latest model can measure absorbance from 190 to 850 nm. Its dynamic range is also very good: from about 0.1 to about 60 in absorbance. Therefore, as long as you don't use an incompatible solvent, you can measure anything that absorbs in this wavelength range. I use it very often for purified proteins. It also works well for turbid suspensions (like bacterial cultures; reading optical density at 600 nm gives an idea of turbidity).

It is easy to use, and of course the low volume requirement is a big advantage. One drawback is that it won't let you fine tune certain parameters like a "real" spectrophotometer would allow (bandwidth, gain, etc.). But you can definitely get decent spectra for characterization of mixtures and concentration estimation of pure samples.


Why most small organisms seem not to be interested in any organic matter which has all moisture removed? On the first glance, it seems that most small organisms do not exhibit any interest in consuming any live or dead organic matter if it is completely dehydrated. Regardless if the food consists of protein, fats or carbohydrates, or any mixture of them, it appears to me that removing water makes bacteria, mould or even insects not consider it food.
Here I consider organic matter which can last for years without being subject to decay by small live organisms:

ghee, made from butter by boiling off all water, lasts for a year or more
freeze-dried food, which still can have 0.5% to 3% moisture, but can last 20 years
honey, supposedly can last forever

While the humble homo sapiens will happily put freeze dried milk in his mouth, most small organisms seem not to have any interest in organic matter with ultra-low moisture:

bacteria
mould
and to a certain extent even insects

For example I noticed ants will quickly gather around any drop of fat used in cooking, which has moisture and other impurities, but will ignore clean, dry ghee.
Why is moisture removal such an universal protection against small organisms and where exactly is the boundary between organisms which can't consume dry matter and the ones which can? Are there any known microorganisms which will consume completely dry organic matter?

TL;DR
If it doesn't last forever this is some organisms consuming it. It is a matter of ecological niches, what are the requirements (humidity, temperature, etc.) to live and reproduce
I believe we should separate the discussion in two: small organisms and microrganises
Microorganisms
Microorganisms that consume our food need to get there, either they got there from the air or they are already there. Other vectors can be insects, animals, water and soil but since this discussion is about food and we tend to keep our food protected from those vectors I'm going to ignore them.
Most of the microorganisms of interest (Bacteria, Archaea, Fungi & Oomycetes) exist in air as spores. This are analog to seeds, they are alive but inactive and need to arrive to a good environment to sprout. Spores can survive for many years, even millions of years("Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber". Science. 268 (5213): 1060–1064.). This survival mechanisme includes dehydration and therefore rehydration is necessary for sprouting.
In addition some of these (mainly oomycetes) need free-water to live & reproduce while others require some levels of moisture.
Dehydrated organic material tends to be hygroscopic. Thus if the non-spore form of the microorganism lands on it the organism will probably loose water and die.
Microorganisms, like every organism, have niches they occupy. One of the characteristics of these niches is the temperature. Freeze-drying includes freezing which lowers the temperature below the survival temperature of many microorganisms and preserves the food. Microorganisms that grow in low temperatures grow slower so it will take more time for us to notice their presence. They still require water so the combination of freezing and dehydration provides a good protection.
Honey has a antibacterial activity in it preventing growth of microorganisms. In addition honey contains a lot of sugar and other molecules making it hypertonic to most microorganisms causing them to loose water if they land on it. Also his high viscosity prevents the free movement of microorganisms.
Small organismes
Many small organismes still need water to live and reproduce (like nematodes)
Insects are highly specified to their environment and food intake. They might not be able to consume dehydrated food.
In addition, as mentioned in the comments by Kal

a lot of these small organisms who are not interested in completely dehydrated "food" would also be ones who
don't explicitly drink water (at least, not enough).[...] For organisms that
don't explicitly drink water, their major source of water would come
from the food. So if the food doesn't contain enough water, they don't
bother.

Ants and other insects do eat dehydrated organic material like seeds, but it still has around %10 moisture
Oil is not hydrated but liquid, since it is oil and not water


Why does protein folding not depend on the order in which it is synthesized? I read an article recently, written by researcher from Department of Biochemistry, University of Washington, which stated that:

  Similarly, success in de novo protein design bears on the question I get after every talk about the importance of the order of chain synthesis on the ribosome to protein folding; computational protein design calculations completely ignore the order of synthesis which hence cannot be critical to protein folding.

I was wondering, how could it be that the form that the protein is folded to, does not have anything to do with the amino-acid sequence that constitute this protein? What I mean, is in case I look at mirror image of a protein, would it fold the same? if I consider for example the sequencers: ser-gly-ala-glu-pro-asp and asp-pro-glu-ala-gly-ser, will they both fold the same? (I think those are d-protein and it's l-protein counterpart)

Can anyone provide evidence that this is, in fact, so. Or do I misunderstand the section quoted?

link to the paper: sci-hub.tw/10.1002/pro.3588

I suspect the author meant something a little different. It's not just that it doesn't matter if a protein is synthesized from N- or C-terminus it's also not important for the end result of folding that the synthesis is gradual at all.

When designing proteins de novo they model the folding on a computer. The gradual addition of amino acid residues to the protein is not part of these models, the computations are made on the entire sequence at once. Still, when the designed proteins are synthesized on ribosomes they fold correctly. So the fact that the proteins are built step by step shouldn't influence how they are folded very much. As long as there is a sufficiently low free energy state it will be achieved.

Also, N-ser-gly-ala-glu-pro-asp-C and N-asp-pro-glu-ala-gly-ser-C are not exactly the mirrored images of each other. They just have terminal amino and carboxyl groups swapped. I imagine this can influence folding a bit.


What is an "open system" when it comes to PCR machines? I have heard the term "open systems", such as here when it comes to RT-PCR machines, but I'm not 100% sure what this means, does this mean machines you can purchase yourself? Such as this one? ... compared to one that would be in a lab?
Also, I have heard that they come with the statement that they are for research purposes only and should not be used as a diagnostic tool, is this because anyone can buy them?

In an open system, "mRNAs are detected because of their property of being expressed in the tissue sample isolated for study. This approach is in contrast to what are called closed-system approaches, in which the mRNAs to be detected are selected as candidates in advance of analysis; a contemporary example of a closed system would be a gene “chip” hybridization experiment." [Sutcliffe, J.G. (2001) J. Neurosci. 21:8306-9. “Open-System Approaches to Gene Expression in the CNS”] https://doi.org/10.1523/JNEUROSCI.21-21-08306.2001


What causes a small bump in the arterial pressure plot? In my book there is a plot of the arterial pressure against time.

From the plot, during heart contraction, there is greater pressure on the artery and during heart relaxation, there is lower amount of pressure on the arteries.

This makes sense because P = F/A, the surface area of the heart is smaller when it is contracted versus when it is relaxed, hence greater pressure.

But why is there a small bump while the pressure is decreasing from systolic pressure to diastolic pressure?

This bump is related to the closure of the aortic valve as a reaction to the retrograde blood flow which in turn gives small change in blood pressure.


How does coconut water solidify into hardened coconut meat? At first, the coconut is filled with liquid endosperm. Later when it ripens, the outer layers form brown fibrous covering, and the inner solid layer turns brown and hardens. Within that, a white layer forms (which is soft and thin at first and then gradually hardens and thickens). After ripening, there is a white layer with very little fluid. So, it's gotta be the liquid endosperm which has hardened over the course of time to form the white layer. So, how does it harden?

There are three types of endosperms encountered in botany - nuclear, heliobial and cellular. The endosperm of Cocos nucifera is both special and interesting.

Initially, the cocunut is a nuclear liquid endosperm. Meaning, it is a coenocytic liquid tissue with lots of rapidly dividing nuclei. The reference I cite here (although pretty old), states that it is safe to assume the fluid to be the 'sol' phase of cytoplasm. At some point, gelification of the sol surrounding the nuclei occurs and cellular boundaries start to appear.

These cells and nuclei start to settle down on the endothelium (inner lining of the integuments) and the cells divide to produce a columnar sort of a covering over the it. This is what forms the characteristic coconut meat. Development of the cellular endosperm is by coalescence of these deposited cells and nuclei at the antipodal end (bottom end of the fruit) and continues towards the top end. You might have noticed that the meat is thicker at the bottom but thins out towards the top.

The cells right above the endothelium stay meristematic for a long time while the columnar cells on top of this meristematic layer grow radially inward.

If the terminology seems confusing, the bottom end is the antipodal end. End. in the diagram stands for endosperm - the coconut meat. The Sh. is for the shell, which is the thickened inner integument. The inner lining of this shell has been referred to in this answer as the endothelium. Mic. stands for micropyle where the stalk (pedicle)  of the fruit is. It is at the micropylar end that the embryo is placed. Remember! The coconut meat is not the growing embryo.

How does the meat harden?

As said, initially the deposited mass of cells and nuclei is jelly like and slowly hardens after proper cell wall synthesis etc. The hard white coconut meat that can be grated, is end stage of maturation and is formed when the above said tissue architecture has been established.

What happens to the coconut water?

After the cellular endosperm has reached its final state a little water is still left in the coconut. This water is opalescent compared to the clear water found in younger fruits. Interestingly this water is now totally devoid of nuclei.

  Whether the decrease in liquid is the result of its incorporation into the endosperm cells or due to evaporation due to drying and cracking of the pericarp remains uncertain.

Sorry for the anticlimax. But this has been quoted from a 1955 paper. I was unable to find newer papers. Little work has been done in morphological botany in the recent past, but I'm pretty optimistic the answer would lie somewhere in literature.

References:

V.M. Cutter, Jr., K.S. Wilson and B Freeman. Nuclear Behavior and Cell Formation in the Developing Endosperm of Cocos nucifera. American Journal of Botany (1955), 42 (2), 109-15.
A. Abraham, P.M. Mathew. Cytology of Coconut Endosperm. Annals of Botany (1963), 27 (3): 505-512.
The Hindu (2002) : Mystery behind coconut water, R. Subramaniam.


What's the best way to measure biodiversity? As I understand it there are various ways biodiversity is measured, with varying results. From what I have been told on these boards, part of the difficulty is because it's hard to define a species exactly, so it's hard to count them.
What I really want to know is whether genetically engineered organisms count towards increased biodiversity but my last attempt at asking that question foundered on the rocks of species definition.

A very good way to measure biodiversity would be to do environmental barcoding with high-throughput sequencing methods, and then use an algorithm that estimates genetic distance to get both species count estimates, and then calculate higher-level diversity, such as genera and families. Then you would repeat this procedure over several collections to obtain a species accumulation curve, so you could then estimate the asymptote. The future possibility of biogenereed organisms would not be worth reporting among the thousands of species at a given location.


How does PCR mutagenesis add restriction site near the gene of interest? I have been learning about PCR mutagenesis to add restriction site right next to the gene of interest using a primer that's attached with single stranded restriction site (first image). I have drawn my own diagram (second image) to better understand how this works, but I am stuck at the last step in question mark. How does DNA Polymerase 'insert' the green sequence (restriction site) so I would end up with the gene shown in the bottom?
Thanks for anticipiated response.

[![enter image description here][3]][3]

This diagram would be easier for you to conceptualize if you instead used the actual nucleotides in the restriction sites and green GGAGAA region along with your gene of interest (GOI). I recommend working with the DNA sequences when learning about primer design for various applications. I believe it has led you to be slightly confused with what is the restriction site and what is not in this diagram so I'll walk through it.
At the first step shown, you have your annealing region of the forward and reverse primers binding to the GOI. The overhanging region on each primer contain your restriction sites, which are flanked by the GGAGAA region for these restriction enzymes to have a sequence to "grab on" when you perform a restriction enzyme digest. Note that the annealing region of your primer anneals to the GOI because it has homology to the DNA sequence. Your restriction sites and green "clamping" region do not have homology to your DNA template so they are considered the overhanging regions. It is important to have your annealing regions of both primers of similar annealing temperatures when designing this or you may not have an efficient PCR reaction. I typically use this tool from NEB to design annealing regions of my primers. https://tmcalculator.neb.com/#!/main
Moving forward, these primers are both going to be used in one PCR reaction, not separate. Thus, when the reaction begins, the double stranded DNA template will denature, giving your forward and reverse primers the opportunity to anneal during the annealing phase of a PCR reaction. During the elongation phase, your DNA Polymerase will add complementary nucleotides in the 3' direction of your primers. Now after the first cycle, you have two different products. The forward primer's product has the GOI with a single stranded BamHI overhang on the 5' end, while the reverse primer's product has the GOI with a single stranded NotI overhang on the 5' end.
During the second cycle, after denaturation, the reverse primer with a NotI overhang anneals to the forward primer's previous product with a BamHI overhang. The DNA polymerase then adds nucleotides in the 3' direction of the primer, eventually adding complementary bases to the BamHI overhang. The same is done vice versa with the forward primer and the reverse primer's previous product.
Now after the second cycle, you have the desired products which will be amplified exponentially. Your GOI flanked by NotI and BamHI restriction sites with the GGAGAA region on both sides. This product is ready for a restriction enzyme digest.


What happens to the language processing brain part if no language is ever learned? Language is processed in the human brain in multiple regions.
Some of them seem to be used exclusively or mainly for language processing,
other regions are distributed overlapping with other functions.

If a feral child is never exposed to any language, and therefore never
learns one: What happens to the language related parts of the brain,
like the ones exclusively used for language?

The language processing is not the central point - so feel free to use analogous examples of brain regions that are unused based on exceptional circumstances. Blindness from birth on comes to mind. Also, no need to base examples on homo sapiens.

Although this specific experiment wouldn't be done, similar experiments have been done in experiments in animal models where a sensory input is removed/altered. These experiments show that if you remove some sort of sensory input, the parts of the brain originally responding to that input will take on other tasks. There have been many studies that show this, but the canonical reference is often this one, where the part of the brain previously responding to sensory input to a finger instead responds to stimulation of another finger after the original finger is amputated:

Merzenich, M. M., Nelson, R. J., Stryker, M. P., Cynader, M. S., Schoppmann, A., & Zook, J. M. (1984). Somatosensory cortical map changes following digit amputation in adult monkeys. Journal of comparative neurology, 224(4), 591-605.

There have also been studies of humans with sensory deficits like blindness or deafness that show similar reorganization, depending on the age the deficit is acquired. For examples, see:

Finney, E. M., Fine, I., & Dobkins, K. R. (2001). Visual stimuli activate auditory cortex in the deaf. Nature neuroscience, 4(12), 1171-1173.

Kujala, T., Huotilainen, M., Sinkkonen, J., Ahonen, A. I., Alho, K., Hämälä, M. S., ... & Salonen, O. (1995). Visual cortex activation in blind humans during sound discrimination. Neuroscience letters, 183(1), 143-146.

In summary, the result is that the neocortex is a very flexible, adaptable structure, and if inputs of a certain type are impoverished, that region of the cortex is used for other purposes. Essentially, neighboring functions creep in to that space.

Language processing in humans includes both auditory areas that respond to the sounds made by language, and premotor processing areas that seem to be important both for understanding the semantic content of language and for producing verbal output. None of these areas are truly language-unique, though, they are just regions that are active more than other areas when language-based tasks are occurring. In a person not exposed to a language, it's likely they would develop some rudimentary language-based skills anyways unless they were truly raised in some sort of sensory deprivation context - at this point an answer would get too far into speculation. Besides that, those areas would probably be re-purposed for other types of sensory processing and other types of motor planning.


How to selectively breed a plant? Let's say I ordered seeds of a plant online. Then, I plant the seeds and grow a few plants. Then I take the seeds that the plants produced and separate them based on each plant.

Is it possible that I could then use those seeds to continue growing plants that have a desired characteristic? For example, if I wanted to grow taller and taller plants could I just keep planting seeds from the tallest plant? Or would I need to use a different method or technology to do this?

Yes, just planting seeds from the tallest plants would already do great. You could just chose an arbitrary size threshold under which you discard the seeds and above which you plant the seeds. Or you could plant all the seeds of the largest plant, almost all the seeds of the second to largest plant, all the seeds of the third largest plant etc... If plant height is a heritable characteristic (and it certainly is) then you will see a result after a few generations only.

You might want to ensure you understand the definition of heritability and the basics of quantitative genetics by reading the post Why is a heritability coefficient not an index of “how genetic” something is?.

Now instead of picking a random threshold for selection, you could be smarter and make some calculations. If you were to perform too a strong selection pressure (such as growing the seeds of the tallest individual only), then you will very quickly reduce genetic variation for height to zero and therefore remove all heritability. If you are using not a strong enough selection pressure, then you might barely see any changes even if you go on for many generations. Estimating the right type of selection pressure depends on the specific population you are facing (typically population size) and to its evolutionary history (typically previous selection on height or correlated traits and past population size).


Is it wrong to consider an allosteric inhibitor a non-competitive inhibitor? Supose Caspase-1 is allosterically inhibited. Since the inhibitor is not binding in the active site but instead in the allosteric binding site, can I conclude it is a non-competitive inhibitor?

No, you cannot assume that an allosteric inhibitor is non-competitive. "Allosteric" refers to the location of binding, whereas terms like competitive, non-competitive, uncompetitive, or mixed inhibition refer to how (or if) the binding of the inhibitor affects binding with the substrate.

The Wikipedia page on competitive inhibition is a reasonable source for this question.

A competitive inhibitor is one that prevents binding of the normal substrate(s) at the active site. It is possible to achieve this either by literally getting in the way by binding in the active site or by binding elsewhere, causing a conformational change that prevents binding the active site. Both cases are considered competitive inhibition because of how they influence substrate binding.


Are bears related to dogs in a similar way to how cats are related to 'panthers'? I've tried searching on Wikipedia but I couldn't find what family dogs belonged to. Ursidae is 'bears' and Canis is 'dogs' ; Panthera is big cats like:- tigers and jaguars is what I know.

No, because panthers are cats, but bears are not dogs. You can see their phylogeny in a figure from one of my papers here: https://www.researchgate.net/figure/Most-likely-phylogram-derived-from-the-Bayesian-Analysis-ln-533753675-Numerals_fig1_6550244

As you can see, Bears are most closely related to pinneped (seals and sea lions), with dogs as sister to that group.


Transcription rate expressed in microarray per hour This article gives measurement of transcription rate  and the unit they're using is microarray per hour.

For example, at 27°C the average expression of their genes is 236.1 microarray per hour (page 4). What does this unit mean? Given that each DNA spot in a microarray contain 1 picomole of DNA (wiki), does it mean that the gene is transcribed into 1 picomole of RNA (or of nucleotides?) per hour? Or does it mean that 236.1 RNA are created every hours?

The units here are relative units of intensity.  There may be about a picomole of probes on a microarray spot, but the units of intensity are not scaled to the precise concentration of DNA on the spot.

There are many variables which make exact measurements of intensity difficult to translate into the number of RNA bound to a spot.  The main one is nonspecific or non-target binding.  The oligomer on the array surface is typically between 25 and 50 bases long - it isn't the entire length of the RNA being tested by a given spot.  Another RNA may have some or most of the same sequence as a probe, or some labelled RNA will tend to get associated with some spots.  Usually factors such as the position of the spot on the array surface, the GC composition of the probe and variations in the batch of RNA preparation will also cause the intensity to vary.

Still, even with all this, with the same prep conditions and with an identical set of arrays, its valid to look at the intensity over time.  In this paper, the investigators took array measurements at different time points and at two different temperatures after 4-Thiouracil  is added to the cells, which allows one to follow RNA produced by transcription at a given time.

Since the units are arbitrary but still proportional to the mRNA found in the cells, a difference experiment like this is valid, even if the absolute concentration of any given RNA is still a bit of a mystery.


Does introgression require interspecific hybrids to be fertile? How is this possible? Wikipedia says that Introgression, also known as introgressive hybridization, in genetics is the movement of a gene (gene flow) from one species into the gene pool of another by the repeated backcrossing of an interspecific hybrid with one of its parent species.

Does this mean that the interspecific hybrid is fertile? But is it possible, that an interspecific hybrid is fertile?

Does this mean that the interspecific hybrid is fertile?

Yes

  But is it possible, that an interspecific hybrid is fertile?

Yes

You might be confused by the idea that by definition two individuals from different species should not be able to interbreed. If so, then you should have a look at How could humans have interbred with Neanderthals if we're a different species?.


What does common viruses found in the body weigh? On NPR public radio news it was said that if the bacteria that is natural that assist in body function or just present in your body was put it into a ball it would weigh more or less 7 ounces (approximately 200 grams). I tried to find the exact quote but am still looking for it and will revise when I find it.

Can viruses assist in body function as in extending life in any way?

Can a body be 100% free of viruses of not how much would the total virus weigh if put in a ball?

Viruses, in general, are obligately pathogenic i.e. they don't usually co-exist (as commensals or symbionts) with our body cells. Their mechanism of survival involves usurping of the host cell machinery to produce their own proteins and genetic material. However, as pointed out in the comments, there are some viruses such as the GBV-C which can infect the host but seldom cause any disease. Moreover, this virus has been shown to have a positive effect on the innate immune response and inhibitory effect on HIV [1].

(Also, have a look at: Do beneficial viruses exist? If so, what examples are there?)

In our genome, here are some remnants of viruses that had infected our ancestors long back in past. A prominent example is that of retrotransposons. Retrotransposons are DNA sequences that constitute a significant part of our genome and they are structurally similar to the genome of retroviruses (like HIV). Retrotransposons had been considered junk DNA in the past but recent studies have shown that they do play some important roles in our body. For example, L1 retrotransposons cause somatic diversity (genetic diversity at the cellular level) of neurons and may possibly contribute to increasing the plasticity of our brain[2,3]. Retrotransposons can also regulate gene expression[4].

Other than that, there may be infectious viruses that are present in the body but are dormant. These may become active later (when the conditions are conducive) and cause the disease in that individual or spread to another person.

You can perhaps calculate the weight of these viral remnants (retrotransposons). It won't provide any great insight to anyone. You just have to calculate the percentage of genome these DNA sequences occupy and multiply it with molecular weight of the genomic DNA and total number of cells in the body. I'll leave that exercise to you.


why does translation occur more frequently than transcription? In our textbook it says that translation occurs more in a cell than transcription but I couldn't find anything that explains why it happens

The simple answer

Under the assumption that each mRNA molecule is translated at least once, by necessity translation will happen more often than transcription. This is because the only way to get a protein is to translate an mRNA.

In other words, as long as there are more protein molecules (translation products) than mRNA molecules in a cell, then the process of translation must have occurred more than transcription.

One estimate of the ratio of protein molecules to mRNA molecules given here is on the order of 100-1000 for E. coli. ("Under exponential growth at medium growth rate E. coli is known to contain about 3 million proteins and 3000 mRNA (BNID 100088, 100064). These constants imply that the protein to mRNA ratio is ≈1000, precisely in line with the estimate given above.". [MP note: the numbers quoted are actually closer to ~400K and ~1.4K, so this is not completely accurate; the source paper itself estimates between $10^2-10^4$ for the same ratio of protein to mRNA. Note though that the yeast cell estimates are even higher.]) So there are likely between 100 and 10,000 times as much translation as transcription events.

The speculative answer

From the perspective of "why" this is the case in terms of why cells might "choose" to have this ratio of proteins to mRNA (accepting that it must be true based on the ratio of protein to mRNA), we might say that proteins are useful and mRNA is not. Therefore, it's better to have more proteins (implied but not stated by @mgkrebbs comment). Or rather, mRNA is only useful because it gets you proteins, which are useful.

So it "makes sense" for cells to minimize the amount of energy put into generating mRNA and maximize energy put into making proteins. But that's human logic projected onto the cell, we can't know that that is the logic for why cells do what they do (or evolved to do, or whatever).


What kind of ants are these? Are these venomous? I found these ants on a small mango tree in front of my home. Could someone identify them for me.

Length: 2-3 cm

Location : North India(Chandigarh)

Temperature: 21-24 degree celsius

More info: They built a home out of leaves of the tree.

These ants are called weaver ants, they are in the genus Oecophylla.

'Helcium is attached relatively high on abdominal segment III only in Oecophylla'
http://www.antwiki.org/wiki/Formicinae

They use the silk produced by their larvae to bind leaves together to make chambers for their brood. As any ants in the Formicinae subfamily, they do not have a stinger. They can however bite and drop formic acid on your skin, which can cause irritation. They are used in orchard as biological control agents against pests.


By what mechanism do cephalopods regrow limbs? As far as I can tell, there are two types of limb regeneration: epimorphosis and morphallaxis. Epimorphosis is used by animals such as amphibians and various phyla of worms, while morphallaxis is used by hydras.
I have been trying to find out which of these mechanisms is used by cephalopods, and no reliable source paints a clear picture one way or the other. Can anyone here help?

well gastropod mollusks use Epimorphosis, so it is likely cephalopods use the same mechanisms. Basically all triploblastic organisms use this mechanism so phylogenic bracketing points towards it as well.
morphallaxis is generally restricted to very simple organisms.
Regeneration of the visual system in gastropods (Mollusca)
Oksana Tuchina  Victor Benno Meyer‐Rochow
Neural regeneration in gastropod molluscs
Author links open overlay panelStacia B.Moffett
Regeneration of the visual system in gastropods (Mollusca)
Oksana Tuchina  Victor Benno Meyer‐Rochow (alternative link)


Why don't self pollinated crops show inbreeding depression? Being continuously self pollinated means the fusion of same/similar genes from time to time, then why don't they show such a decrease in productivity?

Yes, self pollination does lead to inbreeding depression:

  However, we found substantial inbreeding depression, with seeds per fruit, progeny survival and progeny growth being lower after self- than after cross-pollination. Progeny arising from self-pollination also had a higher frequency of certain traits ... which were associated with lower rates of survival. ... high inbreeding depression has also been reported in other self-compatible trees ...

--Self-pollination and inbreeding depression in Acacia dealbata: Can selfing promote invasion in trees?

  Inbreeding depression is one of the leading factors preventing the evolution of self-fertilization in plants.

--Inbreeding depression in self-incompatible and self-compatible populations of Leavenworthia alabamica.

  The strategy for breeding F1 hybrid squash is to develop parental lines through self-pollination. However, it increases plant mean homozygosis, which is not the natural genetic state of a cross-pollinated species, and can cause "inbreeding depression".

--Depression by inbreeding after four sucessive self-pollination squash generations

So why don't all crops that self-pollinate show decreases in productivity? In part, they do, but the reduction in productivity caused by inbreeding is outweighed by the increases in productivity caused by inbreeding (i.e. selection for productive traits via inbreeding leads to both positive and negative results, and the total outcome is the sum of the positive and negative effects).

And partly because the deleterious effects of inbreeding can be partially overcome through "purging". The negative genes that lead to inbreeding depression when homozygous can be removed from a population as the affected individuals die (or fail to breed) and take their negative genes with them. Purging is most common when a population has a moderate degree of inbreeding over a longish time, which is what you'd expect with a crop that typically self-pollinates. It's an effect in many but not all common crops:

  Several plant species, E. g alfalfa (M. sativa) carrot (D. carota) , hayfield, tarweed etc show very high inbreeding depression. ... Many crops species, such as maize, jowar, bajara etc. shows moderate inbreeding depression. ... Several crop plants, E. g onion (A. cepa), many cucurbits, rye (S. cereale), sunflower (Hannus), hemp etc show only a small degree of inbreeding depression. Only a small proportion of the plants show lethal or subvital characteristics. The loss in vigour and fertility is small; rarely a line cannot be maintained due to poor fertility. The reduction in yield due to inbreeding is small or absent. Some of the inbreds lines may yields as much as the open pollinated varieties from which they were developed.

--Degree of Inbreeding Depression


Auxotrophic complementation test with yeast If auxotrophic strains grow on minimal media do they complement each other or not?  Also, is complementation the same thing as complementing each other?

If the yeast strain A is auxotrophic for AA 1 and the yeast strain B is auxotrophic for AA 2, neither would be able to grow in minimal medium by itself. But combined they complement the lack of AA1 in strain A by strain B and vice versa. That is metabolic complementation.


Long term liquid food diet by blending/grinding all quality foods one would normaly eat, not any weight loss or prepared drinks I want to know what are the effects of not using your teeth to grind foods but preparing it before eating with blending and grinding them into a liquid.

Here I am not talking about any weight loss or fitness industry prepared drinks. I mean the ordinary raw and cooked foods like meat, vegetables, cereals, and fruits that one would normally eat in classic meals.

Would this decrease of work done by teeth and digestion system have positive or negative health effects?

I was in a car accident age 19. Jaw was wired shut, food access was limited to one broken front tooth. It was liquid diet or nothing.
 So, I drank a lot of foods in liquid form, ( soups, etc. ) and a lot of Gerber's baby foods, and just about anything that could be pulverized in a blender.
 I gained weight like crazy. About 15 pounds in 2 months.
 The body takes advantage of having the harder work of digestion done for it. One of the advantages of cooking food is it's easier to digest. It is believed by some that such benefits to our life are the reason humans became the dominant force on this planet.


White water bird with black 'hat' The white bird in this picture, swimming between the ducks, was seen in Beijing, China, in januari 2017. It was cold: the water seen in the picture is liquid, but not far from this, the water was frozen. We also saw it standing on the ice.

It has an orange beak with what seems to be a small black spot at its end. It also has black as the top of its head. We did not find a similar bird when searching ducks, goose or even swans. What species is this?

It is a domestic form of mallard. They are bigger, often white or mostly white. Try to google image domestic mallard and you will see the phenotypic variety that domestication has created.

Note the irregular and not symmetrical shape of the "hat" and read the description below from the biggest research center on birds of the world.

Extracted from:
http://www.birds.cornell.edu/crows/domducks.htm

  (...)lots of white is often involved, including all-white breeds like the popular Pekin Duck (...) Usually these white spots are not symmetrical across both sides, and that asymmetry should tip you off to think domestic influence.


Prothrombin time when extrinsic pathway is turned off I was searching for an answer that "why do we need intrinsic pathway when there is fast extrinsic pathway" and i found the answer in the following link:

http://www.pathologystudent.com/?p=3197

It says that the factor X produced in the extrinsic pathway turns off the extrinsic pathway and activates the intrinsic pathway. As the extrinsic pathway is turned off so, we need intrinsic pathway to continue the clotting process. But if the extrinsic pathway is stopped then how do we get prothormbin time because prothrombin time is for extrinsic pathway?

In order to understand the importance of both pathways, you first need to be clear about what is meant by them respectively. Clotting activation from tissue factor (TF) is known as the extrinsic pathway, so you've got that one right.

The intrinsic pathway doesn't involve FX

The intrinsic pathway does not (as often misunderstood) refer to the clotting cascade downstream of factor X (FX) which involves FV, FVIII and thrombin. Rather, the intrinsic pathway is a system which is able to initiate the clotting cascade without any tissue factor being present. It is triggered by the assembly of high molecular weight kininogen, prekallikrein and FXII on collagen. This is also known as contact activation, and sets off a small cascade producing active FIX (FIXa), which can then assemble with circulating FVIIa in order to produce FXa and thereby set off the rest of the clotting system.

The extrinsic and intrinsic pathway are separate ways towards a "common pathway"

So think of it this way: The extrinsic pathway produces FXa in one way (TF), the intrinsic pathway produces FXa in a different way (HMWK+prekallikrein+FXII). There isn't really any interaction between these two. Once FXa is produced from either of these two, it will start to set off what you could call the "common pathway", i.e. it will produce thrombin, which will activate co-factors that will then lead to more production of FXa and propel the entire thing forward faster and faster until it reaches what we know as the thrombin peak.

The intrinsic pathway is not important for haemostasis in humans

Aside from this, you should know that the intrinsic pathway exists, but it doesn't bear much significance in a living human. This is demonstrated by genetic FXII deficiency - you would expect it to produce haemophilia if FXII and therefore the intrinsic pathway was important (just like FVIII and FIX), but it doesn't (read here: http://en.wikipedia.org/wiki/Factor_XII#Role_in_disease).

The principle behind the initiation pathways and the common pathway

So to summarise: You fell victim to a misunderstanding and a bad explanation on that site you linked. The extrinsic pathway doesn't "turn itself off", and the intrinsic pathway doesn't "take over". What really happens in a human is that the intrisic pathway doesn't really do anything. Rather, the extrinsic pathway will produce a little bit of active FXa. But that is enough to produce a little bit of thrombin. And that bit of thrombin will then produce small amounts of FIXa and co-factors (FV and FVIII). These will start to produce more FXa, which will produce more thrombin, which will produce more FIXa and co-factors, and so on.

What the article you refer to is trying to mention are the inhibitory systems that will be set off alongside all of this. Think about it - if thrombin increases its own production perpetually, how does it know when to stop? These systems which ensure that clotting does stop are known as anticoagulation pathways. They are just as amazing as the coagulation pathways themselves, and they are extremely well-geared towards shutting off exactly the right clotting factors at exactly the right time, to ensure that a clot forms in the wound but only there and nowhere else.

Edit: It turns out people do use more complicated definitions of "intrinsic" and "extrinsic" - the problem being once again that everybody can define words as they like. This is rather based on the distinguishing of the two ten-ases, TF-FVII (extrinsic tenase) and FIX-FVIII (intrinsic tenase). In this understanding, the physiological process does indeed start off by the extrinsic pathway (i.e. mechanisms which generate extrinsic tenase), which will kick off the amplification cascade of the intrinsic pathway (i.e. which produces intrinsic tenase). It is true that this way, the contribution of the "extrinsic pathway" is minor once the "intrinsic pathway" is active, but even so, it does not "shut itself off". What turns the extrinsic pathway off is the layer of material which gets deposited on top of the exposed subendothelial surface, preventing access to TF!


Why do I need a flu shot every year, while many other vaccinations last years or even a lifetime? Is it a viral vs. bacterial thing?
Is there just more variety among types of flu than other diseases, so that this year's vaccines don't cover next year's flu?

The flu virus changes rapidly so that the current vaccine doesn't work against the new strains.

The way vaccines work is that they teach our immune system what to look out for. The vaccine contains bits of the virus but in a form that can't cause a proper infection, the body learns what to look for and next time before the virus can really get going the immune system kills it off first.

In the case of flu, every year it looks different enough that the targeting mechanisms of our body don't recognise it. Flu being a RNA virus frequently mutates until it is slightly different. This is called antigenic drift, the changing of the antigens or the parts our body recognises.

On top of that there's lots and lots of types of the influenza virus, that can not only infect humans but others which affect other animals. Occasionally the virus might combine with a random other strain making it completely new: an animal flu and human flu hybrid. These are the epidemics of swine or avian flu etc. This recombination is called antigenic shift.

So each year scientists predict which viruses will affect us this coming year and grow them ready for vaccines. Of course there's some of the old virus floating around looking for someone to infect, but those infected can't be infected by it again if the immune system is working.


Does the fact cordyceps mostly affect insects have something to do with chitin being polysaccharide? This is just a conjecture of mine based on those observations:

Fungus seems to be very good at attacking tough chains of sugars like cellulose and starch.
insects are covered by Chitin, a polysaccharide.
cordyceps only attacks arthropods and in rare instances other fungus. Both arthropods and fungus have chitin in their body.

My initial guess was no but there might actually be some evidence for this. For example, host-switching between fungus and insects apparently happens within relatively small taxa of cordyceps, suggesting that host specialization is not too dramatic.
Moreover, there does seem to be some evidence that chitin is a relatively important metabolic input for at least one cordyceps species.
I don't know that we could say that chitin is the thing that allows the host switching or that it is the most important nutrient for cordyceps or anything like that, but it looks like it at least helps.
It's worth noting that ecological characteristics may play at least as large of a role. The phylogenetic study noted that host switching likely occurred from cicada nymphs (which hibernate underground) to truffles (which have their main mass underground), so it's possibly just an opportunistic jump in the soil environment.
It would be interesting to see if there is a "chitin sensor" mechanism in cordyceps that yields a signal to cordyceps that there is a host to invade. But I don't think that I saw anything that suggests that (though it's far from unprecedented in biology).


What are some examples of genes that code for multiple proteins? The title pretty much says it all. It is widely taught that a gene in a eukaryotic system could produce more than one protein due to post-transcriptional modification, but I do not believe I have come across any specific examples of this. Are any such systems known? Or is this more theoretical?

There are a large number of ways a protein variant can be produced by post translational modification.  The question may seem obvious, but its really quite broad.

I can start this out.  I doubt I know all the ways a single transcript can produce variant proteins.   A detailed description might be more like a review article than an answer here.

First, there are very rare cases of eukaryotic polycistronic mRNA: mRNA which code for more than one protein.  In this case, after translation, the mRNA are processed to make multiple monocistronic RNA.

Then there are proteins with molecules added by covalent bonding to the protein.  Glycoproteins are notoriously variable. Many other small molecules can be bonded to a protein to make a variant of this sort: ubiquitinization, N-acetylation, SUMO domains, lysine methylation are just a few of the more common covalent modifications of proteins.

There are RNA editing which removes some of the coding RNA to make alternative splice RNA.

The list goes on and on. So does any of this come close to what you wanted to know?


Examples of species whose extinct common ancestor is well documented? If we follow the ascendence line of two closely related species we can build a
"Theoretical" common ancestor, whose characteristics were inherited with few differences by the offspring.
         _______ species 1
Ancestor/
        \_______ species 2

Are there examples of extinct ancestors that we can be almost 100% sure they correspond to the ascendant of the two distinct species?
Are these examples well documented with fossils and the inherited traits well understood?

Not with fossils.
Very very few organisms ever fossilize and most of the organisms tissues are not represented in fossils. Less than 0.01% of all animal SPECIES have left a single fossil and most of those have not been found yet.
Because of how incomplete the fossil record is we can never say a species is definitively part of a lineage. in fact the basic assumption in paleontology is that you never have a direct ancestor (individual or lineage) and extraordinary evidence would be needed to demonstrate otherwise.
Only direct observations or high genetic sampling would allow something to be considered definitively a common ancestor at the species level. Now we do have this for some species. We also have fossil localities with really high resolution making common ancestors highly likely, but never definitive.
Part of the issue is also defining species, the definition for species used in paleontology is very different than the one used in say population genetic. Species are nota real things but a human category stuck onto what is basically a continuous spectrum, it only works because most of the spectrum is dead. There is no concrete point at which two groups are definitively separate species. Its a bit like trying to define the exact cut off between two colors. Some groups of biologists favor definitions which increase the number of species others ones that decrease it, and both work because for the actual practice of biology whether two closely related populations are or are not separate species really does not matter.