Can we dilute PureExpress Cell Free Mix to increase number of reactions? Since the PureExpress Cell Free mix is so expensive, I was wondering if it might be possible to just dilute the mix to increase the number of reactions we need to use.
From this image I found:

It seems like by just adding more 3PGA, amino acids we should be able to get more reactions out of a diluted solution. From my understanding, this would mean that 3PGA and the amino acids are the only consumables here. Would diluting just change the amount time it takes for the reaction to occur or is there something else that I'm missing here.

The PURExpress system from NEB is incredibly expensive, for this reason I have avoided it all costs during my experiments with cell-free systems.
This is the paper I've used to create my own cheaper cell-free systems while also discussing reasons why using the NEB PURExpress system is not recommended:
https://pubs.acs.org/doi/10.1021/acssynbio.8b00427

"Although NEB provides a few different formulations of
the PURE system, the commercial system can’t be customized or optimized by the user, and the precise formulation of the commercial PURE system is not publicly available."

This might answer your question as to why I would not dilute the PURExpress system since the precise formulation is not publicly known. Thus, we can hypothesize what would work at various concentrations, but at the end of the day it is unknown what they specifically use in this reaction and how one could optimize it for their own purposes. It would take some trial and error if you really wanted to dilute/change the formulation.

"Our method co-cultures and induces all 36 protein producing E. coli clones in a single flask followed by a single Ni-NTA purification."

This is the method I personally use and it can be time intensive, however the payoff is the cost and ability to optimize your system for your specific experiment.

"The PURE system consists of several different components [7], that can be separated into three main categories: proteins (transcription, translation, and energy regeneration),ribosomes, and small molecule components (salts, buffers, NTPs, creatine phospate, and folinic acid)

If you were to go down the dilution route, I would suggest reaching out to NEB before hand to receive consultation for the purposes of your experiment and any consumables you may need to also purchase. This quote from the paper shows how your system has many considerations for consumables you may need to further research to maximize the expression of certain proteins. As for how this affects the reaction time, dilution shouldn't affect time, it will however affect the amount of product you get out of your reaction.


Why does cyanide inhibit CuZnSOD, but not MnSOD or FeSOD? Different types of superoxide dismutase (SOD) contain different metal ions (Zn, Cu, Mn, Ni, or Fe), all of which allow them to catalyze one reaction, dismutation of superoxide anion, O2−. Cyanide can block this reaction, but only in CuZnSOD.

What is the (bio)chemical mechanism behind cyanide inhibition of CuZnSOD and why doesn't it occur in FeSOD or MnSOD?

I'm just taking a stab, because my inorganic chemistry is rusty.

cyanate (CN-) is well known to bind to iron (it inhibits hemoglobin and causes anoxia), and it also forms a pretty strong complex with Zinc:

http://en.wikipedia.org/wiki/Zinc_cyanide

I would guess that in the case of the SOD that the other liganding amino acids and the pocket of the enzyme are such that the affinity for cyanide is lowered to the point that oxygen can displace it.

In the case of hemoglobin, CN will coordinate to the heme iron in much the same fashion that O2 does, but it doesn't come off.   In the case of SOD, the enzyme will be looking to coordinate to superoxide O2(2-) which would be at a roughly tetrahedral angle to the metal.   This is not a favored geometry for CN coordination, which prefers to linearly coordinate to things.

In the case CuZnSOD it seems likely that this enzyme has enough room and its Zn and Cu binding envirionments don't forbid CN binding. it would be an evolutionary accident really as to why one is sensitive and another is not.

some structures at rcsb:

SODs:
http://www.rcsb.org/pdb/results/results.do?qrid=C0740111&tabtoshow=Current

thiocyanate bound. the pocket is pretty open between the two ions.  no CN bound structure.
http://www.rcsb.org/pdb/explore/jmol.do?structureId=1SXS&bionumber=1


Does knowing the sex of each of a couple’s first N children have any marginal value in predicting the sex of child N+1? Does knowing the sex of each of a couple’s first N children have any marginal value in predicting the sex of child N+1? By “marginal” I mean predictive power beyond other known effects, e.g., the race of the parents, the mother’s weight, season of birth (list from this presentation by Andrew Gelman).

I know that many claims that some variable can predict a child have been accused of resting on shaky statistics (see the presentation linked to above). But the sex of preceding children seems like it could be a strong predictor.

UPDATE: answering fileunderwater's question

  Can you expand on why (by what mechanisms) you think that it could be a strong predictor? Male sex-chromosome bias in sperm?

Yes, sex-chromosome bias was my first thought. I almost focused my question specifically on that but the fact that I saw maternal weight listed as a predictor in the Gelman presentation made me think there might be other relevant factors that I wouldn't think of. So I broadened the scope of the question.

For those who are interested in sex ratio bias itself, the enWikipedia article is pretty good.

As for predictive power, a Bayesian might tell you that by knowing a couple can and did have a male/female should improve, if only slightly, your belief that their next would be the same.  It's by no means predictive and probably largely indiscernible from random chance, but hey it's something!

More to the point, at the very least you might as well just guess their next child will be a son.  As the link above will tell you, the human sex ratio at birth has varied but in general males are more likely to be born - somewhere around 1.03 to 1.08 males per female.  Here's another in-depth study, from 2005, dealing with the last few decades in the US.

That study has Figure 3 (below) and Table 3, which show the raw birth ratio over successive births, and the data are pretty clear: successive births reduce bias.

Those numbers are way more clear than I thought they would - just watch those means move!  I wish there were more information on the variances - clearly there's more down by the 8th child - but that's pretty solid.  Here's another study from Denmark in 1999 doing some of the same stuff (Denmark was popular for this work).  They include the absolutely fascinating Table 2 (below), which breaks down the odds of giving birth to a male given whatever came before.  Which, in the end, is as predictive as you can get, right?

Basically, it's sort of what you'd expect: the more females you have, the more likely you are to have another female; the more males, the more likely the next is a male.  They used about 1.4 million kids but there are some interesting oddities in that table at the extremes.  The best chance for a male?  Your fifth kid, following FMFM.  Best for a female?  Your fifth, after MMMF.

There are some definite issues that can twist the data, particularly when families have another kid to try to get a child of a specific sex.  If you can tease out some of those environmental factors, you'd be better at guessing; still, I wouldn't bet the house on it.  Memorize that table but, when in doubt:

Guess male
Lotta females first?  Maybe guess another one.
A bunch of males?  Guess another male.


Why is an excess number of eosinophils consistent with a violent allergic reaction? What roles do eosinophils play in allergic reaction?

The primary function of Eosinophils is to releas digestive enzymes and destroy extracellular parasites, but they also contain pro-inflammatory molecules and cytokines in their granules.

Eosinophils play an important role in late response inflammation. The primary inflammation is caused by degranulation of improper hyperactivation of mast cells when they encounter antigen/allergen (They have IgE bound to their receptors on a membrane). They release cytokines as IL-4 and IL-13 which recruit Th2 lymphocytes. Th2 lymphocytes release i.e. IL-5 which attract eosinophils.

Eosinophils release the content of their granules, which can degrade the tissue on an organism. Their cytokines attract more WBC - eosinophils (macrophages, TH2 lymphocytes and mast cells) and since this process is not controlled, they accumulate in tissues and it can lead to allergic reaction.

Good book contemplating this topic


Skeletal muscle without antagonist Is there any skeletal muscle that does not have an antagonist? Excluding circular muscles such as around eye and mouth.

The reason why I am wondering is because in biology normally nothing is ever just like that, there is always an exception. This would be the first biological rule without exception that I came across.

I am thinking of humans only for a start but feel free to include any other animal if any have skeletal muscles without antagonists :)

I would argue that the orbiculares do have antagonists. To some extent, levator palpebrae superiorus antagonizes orbicularis oculi, and zygomaticus major/minor as well as risorius antagonize orbicularis oris.

I can think of three muscle that don't have obvious antagonists:

Stapedius
Tensor tympani
Articularis genu

1 and 2 essentially perform the same action, to dampen sounds reaching the cochlea. 3 elevates the suprapatellar bursa.


Multiple clones Sanger sequencing analysis I am doing a 96-well arrayed cloning. I have done Gibson, transformations and minipreps in a 96-well format, then sent out the plate for sequencing. Normally, I sequence 3-4 clones and check if the sequencing looks good manually with Benchling cause it has nice visualization tool that highlights mismatches but also displays sequence quality. Now I have to check the sequences of 96 individual clones. Obviously I can write a simple script that would do alignments and report the alignment quality. However, I am guessing there should be already tools available that work with Sanger clonal sequences and provide nice visualization for many alignments at once. Any recommendations for specific tools I should use?
Thank you!

I haven't personally used it but seqtrace seems to be targeted for this purpose. It seems to be able to do alignments and facilitates multiple trace file analysis.
I worry a little bit about not visually inspecting trace files for sequencing of clones, but I may be a relative dinosaur (about sanger at least).
Here is the abstract:

Modern applications of Sanger DNA sequencing often require converting a large number of chromatogram trace files into high-quality DNA sequences for downstream analyses. Relatively few nonproprietary software tools are available to assist with this process. SeqTrace is a new, free, and open-source software application that is designed to automate the entire workflow by facilitating easy batch processing of large numbers of trace files. SeqTrace can identify, align, and compute consensus sequences from matching forward and reverse traces, filter low-quality base calls, and end-trim finished sequences. The software features a graphical interface that includes a full-featured chromatogram viewer and sequence editor. SeqTrace runs on most popular operating systems and is freely available, along with supporting documentation, at http://seqtrace. googlecode.com/.© 2012 ABRF.


What is meant by Physarum polycephalum having 720 sexes? There is currently some media hype about the slime mold Physarum polycephalum, which will soon be exhibited in the Paris zoo. This was my first time hearing about slime molds, but so far so good.

What I don't understand though is this organism supposedly having 720 sexes. This seems strange to me, as to my – admittedly layman's – knowledge, single-celled organisms like this one aren't supposed to have sexes at all, reproducing instead through cell division. It looks to me like pretty much all newspapers reporting on this have no idea either and decided to just keep it because it sounds interesting. On Wikipedia, nothing is said about hundreds of sexes at the time of writing.

What does this actually mean?

It is true that many/most unicellular organisms such as e.g. bacteria or fungi have no need for sex to reproduce, and can divide by simple cell division. However, sex (defined rather broadly) is a universal feature of life. For example see this review article by Rosie Redfield, which examines exactly what we mean by "sex". The broad definition is just recombination of genetic material, which is a universal (or nearly so) feature of organisms.

It's a little hokey to say that Physarum polycephalum has 720 sexes, as "sex", the idea of a specific category of individuals with regard to reproduction, is different from the biological idea of "sex", when we say "yeast have sex".

What Physarum has, like fungi and other similar organisms, is not really sex, but mating type (see here). Mating type really has nothing to do with what kind of sex organs a fungus has, but rather what fungi have sex with. Certain mating types only have sex with certain other mating types. But this isn't really a one-to-one correspondence like male-female. It's much weirder than that.

There are both "heterothallic" (sort of "single-sexed") and "homothallic" ("hermaphrodite") mating types of the protist, and each organism has a mating type. The homothallic ones don't need other individuals to have sex and make offspring. The heterothallic ones do need other individuals. These mating types are defined not by a sex chromosome like in humans, but by a single gene. When they say 720 sexes, what they mean is that we have found 720 different DNA sequences at the mating type gene which have somewhat different mating behaviors.

I think that your evaluation is correct that the journalists are being pretty inexact here. But I think also that it's important to recognize that basically all of biology is sexual, one way or another.


How realistic is to use DNA for long term storage? This is mainly a followup question to the recent paper Next-Generation Digital Information Storage in DNA.

Personally, while I agree about the data density of the format, I can't help point out the large issues with the inability to rewrite and recopy the data efficiently and potential issues regarding the "immutability" of the data. I'm curious about other takes on the publication and whether or not the stability of the DNA as well as the "writing" inefficiencies are better than I'm believing.

I can at least answer the question about the stability of the stored information. With my colleagues, I worked for several years to estimate the rate of DNA degradation at room temperatures. Our results showed that the information could  be retrieved after 100,000 years storage.


Rationale behind Most Recent Common Ancestor (MRCA)? My main question is this -
I heard Richard Dawkins say in a video that after 1000s of years, any given individual alive today will be either an ancestor to ALL of the humans (in that future time) or none of them. What is the rationale behind this?
I'm unable to find the link to that video. I'll keep searching and add it once I find it.

But my fundamental question is perhaps this - is it necessary that a given species must have at least one common ancestor? I understand that there are multiple common ancestors to humans, the most recent one being MCRA. But could it have been otherwise? I think there's some underlying logic that I'm missing.

I'd appreciate it if someone could answer in a non-technical manner since I know very little about genetics and how all this works.

Update:

Consider the following example. Here's there's heavy inbreeding and as you can see no matter how many generations pass, the population are never going to share a common ancestor from current generation or later. (They could still have a common ancestor from before). But this case violates Dawkins' statement.

But this is an unrealistic example with no mixing and cross breeding. Let's consider another example as shown below. I want to see how the individual A from current generation can be related to all the population in future. As shown in the diagram, although A is related to everyone in some future generation, he is not a common ancestor to all of them. The actual common ancestor belongs to some earlier generation.

For any given no. of generations, theoretically, I could conceive similar lineages by which someone from current generation need not necessarily be a common ancestor to all of the future population (or none). So I don't understand how Dawkins' statement is inevitable.

any giving individual alive today will be either an ancestor to ALL of the humans (in that future time) or none of them. What is the rationale behind this?

It's a simple mathematical observation nothing more than that.

One that doesn't actually require doing any math to understand.

Take a few billion people, let them mix & breed freely within the confines of a limited environment (the world) & eventually (after enough generations) every single one of the current population will be be related & therefore descended from every single one of the original population that have any surviving descendants.

Those whose line doesn't die out will inevitably be an ancestor of every living person at a future generation, eventually.
Those who die with no offspring or have last-descendants do it for them, have no descendants.

It's just a simple statement of something that's obvious when you think on it.


Regulation of the replication of mtDNA at embryonic level While reading an article on mitochondrial inheritance I came across this link.

The results state that mitochondrial DNA replication is regulated in different cells of an embryo at different levels. How is this regulated?

This is a topic which seems to be not very clear yet. References say that this is obviously dependent on the tissue and the "gene dosage" seems to play a role, and that this is probably regulated by a yet unknown factor (see "Mitochondrial DNA replication: what we know." and "Replication and transcription of mammalian mitochondrial DNA.").
Newer articles suggest that it depends also on the transcription of the mtDNA (see "The interface of transcription and DNA replication in the mitochondria." and "Mitochondrial transcription factor A regulates mitochondrial transcription initiation, DNA packaging, and genome copy number."). I will see, if there are other interesting publications, if there are problems with accessing these articles, let me know.


Differences between synaptic connections Consider the following synaptic connections (from here):

axodendritic - A term pertaining to an excitatory or inhibitory synaptic connection between the presynaptic axon of a transmitting neuron and the postsynaptic dendrite(s) of a receiving neuron in a nerve impulse pathway; such connections can influence whether or not a graded potential will be generated on a postsynaptic dendrite.
axosomatic - A term pertaining to an excitatory or inhibitory synaptic connection between the presynaptic axon of a transmitting neuron and the postsynaptic cell body/soma of a receiving neuron in a nerve impulse pathway; such connections can influence whether or not an action potential will be generated in the postsynaptic axon trigger zone at the axon hillock.
axoaxonic - A term pertaining to an excitatory or inhibitory synaptic connection between the presynaptic axon of a transmitting neuron and the postsynaptic axon hillock or axon of a receiving neuron in a nerve impulse pathway; such connections can influence whether or not an action potential will be generated in the postsynaptic axon trigger zone at the axon hillock.

What exactly are the differences between the connections in terms of their influence on the neuron?
To my understanding:

axodendritic: influences a dendrite $\rightarrow$ hence influences the graded potential of the neuron
axosomatic: influences the graded potential of the neuron directly
axoaxonic: influences the axon only (independently of the neuron?)

Hence, to my understanding the axodendritic and axosomatic connections yield the same result: they influence the graded potential of the neuron (e.g. whether the neuron "fires"), where the axoaxonic connection only influences whether the axon fires. Is this correct?
If so, then what is the purpose of dendrites? If axons can connect to the cell body directly, then why would they need dendrites (apart from yielding a larger connection surface to the neuron)?
Note: I have read this answer, which partially explains the use of dendrites. However, it also states that the signal decay due to the synaptic location is compensated for by the local potential change. Therefore, IMO, the answer states that the main advantage of having dendrites is that inhibitory axosomatic synapses can capitalize on the location-dependence of the axodendritic synapses. Is that the true and only purpose of axosomatic synapses? (Please, correct me if my inference is wrong!)

Neurons are all about specialized structures having specialized roles. You've given a good justification for dendrites---an efficient way to fit lots of connections in a small space. A pyramidal neuron in cortex, for instance, will have tens of thousands of synapses. If you only had axosomatic connections, the soma would have to be enormous to fit all of them (and this would cause lots of other issues).

Dendritic structure also allows the cell more efficient electrical properties (see cable theory) and to process inputs independently. In fact, different parts of the dendrite are now thought of as independent computational compartments. For instance, the cell might want to selectively strengthen a single synapse or all the synapses on one dendritic branch. By physically isolating those synapses in small dendritic structures, it is easier to make those targeted changes without unwanted "crosstalk" on other synapses or cell activities. What's more, incoming connections from different areas often segregate into regions of the dendrite (e.g. in CA1 hippocampal pyramidal neurons, cortical connections to the most distant part of the dendrite, internal hippocampal connections to the part of the dendrite closer to the soma).

When a cell has a large dendrite (some neurons have no dendrites), its useful to think of axodendritic synapses as the normal inputs that contribute to fine-grained computation, and axosomatic and axoaxonic synapses as more global gates. These latter types take advantage of their location to short circuit the "normal" computation in the dendrites. An inhibitory axosomatic synapse, for example, will reduce the effect of all dendritic inputs when activated.


Length differences between physically interacting proteins What can be said on the length differences between interacting proteins? Are they usually of similar sequence lengths or not at all?

At least in a human protein interaction network, it appears that proteins indeed mostly bind to proteins of similar sequence length. Consider the figure below, based on analysis of a human protein interaction network from the Protein Interaction Network Analysis (PINA) platform. In the data set, the median relative protein size (the largest amino acid sequence length divided by the smallest in each interacting pair) was 1.9, the maximum value was 293.6 and the 99th percentile, which is the cutoff for the plot, was at 15.2.

Edit: As per stords comment below, you get essentially the same result for a random network:

In this case, the network was generated by picking two proteins at random from the original network, creating an interaction between them, and repeating until the random network has the same number of interactions as the original.

Immediately, it might look like the PINA PIN is dominated by random interactions. I would run some network analysis to determine its characteristics, but seeing as it's a rather large network it would take more time than I have right now. The results are similar for two additional networks with interactions in Saccharomyces cerevisiae and Caenorhabditis elegans respectively downloaded from PINA. Note that all three networks have been constructed from databases with varying levels of curation (See the original publication for PINA:  http://www.nature.com/nmeth/journal/v6/n1/full/nmeth.1282.html). As such, many of the interactions might not be biologically meaningful.

Taking into account the above, you might want to define "interacting proteins" more precisely. One might expect that a better curated network only containing interactions with a known function or effect might give a different picture. However, using a more strigently constructed human "functional interaction" network published by Wu et al. (http://genomebiology.com/content/11/5/R53, FIs_043009.txt in Additional file #3) still gave a similar result.

Method: I made a Python script to calculate the relative amino acid sequence lengths for all interactions in a human protein-protein interaction network (PIN) available from PINA ((http://cbg.garvan.unsw.edu.au/pina/interactome.stat.do). The network file is located at: http://cbg.garvan.unsw.edu.au/pina/download/Homo%20sapiens-20121210.sif. PINs for other organisms are also available at the same site and many other places. The script can be used with any PIN in SIF format using UniProt identifiers.

The script can be downloaded here: https://github.com/jarlemag/misc-bioinformatics/blob/master/ProteinInteractionNetwork.py

The most time-consuming part was downloading the sequence lengths from UniProt. To avoid having to do that, the protein sequence lengths can be saved to and loaded from a text file.  The list of protein sequence lengths is here: https://github.com/jarlemag/misc-bioinformatics/blob/master/protlengths.txt To create the figure, place all three files in the same directory and run the script using Python 2.7.

Keep in mind that the PIN data may not be entirely reliable.


Reusable microarray chips Microarray chips allow us to conduct many expression experiments in parallel to each other but they can be used only once as far as i know. Are there reusable microarray chips? Have people ever tried it? If there are, are they becoming more common? If people do not choose to use them even though they are in the market, what can be the reasons?

As far as I am aware, there are no commercially available re-usable microarrays. The reason for this is most likely that the arrays are really sensitive and you run into the trouble with false positive signals. I have once seen a microarray which has been stripped and still delivered quite some signals in areas which had a strong signal before.

You have to make sure to strip all the hybridized samples from the chip without damaging the probes which are bound on the surface. I think the trade-off between "everything is off" and "some sample is still bound" is not good enough. Who wants to risk false positive signals and possibly retract publications on this basis? You may also loose weak signals which are hidden under false-positive signals.


Evolutionary elimination of recessive gene As recessive gene is suppressed, why over millions of year of evolution have not wiped them away completely, why don't they just go extinct, as people with those genes go extinct?

Simply put, there may not be enough selective pressure to force those alleles out of the population. For example, take a hypothetical gene for eye color. The dominant allele gives brown eyes, the recessive blue, due to the lack of expression of a certain pigment-processing enzyme. So, two heterozygous (brown-eyed) organisms are crossed:

   |  A |  a |
--------------
 A | AA | Aa |
--------------
 a | Aa | aa |
--------------

which results in 75% brown-eyed offspring, and 25% blue-eyed offspring. Unless there is some very strong factor in the environment that has a negative selective pressure on blue eyes, the recessive allele will remain in the population.

OK, that's for an allele with no negative pressure acting on it. What about a disease allele, for example one that has a point or other mutation inactivating an essential enzyme, such as iduronate-2-sulfatase (I2S), a key enzyme involved in the breakdown of waste in the lysosome. It is part of a group of diseases known as lysosomal storage disorders, and is the causative agent of Hunter Syndrome.

People who have the so-called "wild-type" allele(s) of I2S have normal function, even if they are heterozygous. However, if two heterozygotes produce offspring (or if a heterozygote produces offspring with a homozygous recessive individual), then there is a chance of a child with two recessive or defective forms of the enzyme, and they are much more likely to develop Hunter Syndrome (almost no genetic disease is 100% penetrant). If untreated, this disease can have many quite horrible effects (especially given that it usually appears in childhood). The disease is also progressive (it gets worse the older you get), and while it in itself does not typically cause death, patients have (sometimes severely) limited lifetimes.

So why haven't the mutant, disease-causing forms of I2S been "weeded out" by natural selection? In a single word: heterozygosity. Studies (I don't have a reference, unfortunately) have shown that supplying a Hunter patient with as little as 10% of the typical amount of active enzyme in an unaffected person is enough to resolve the acute symptoms of the disease, and begin reversing many of the long-term effects. All things being equal, one would expect that a heterozygote carrying one functioning allele of I2S and one mutant allele would express about 50% of the amount of enzyme that a completely unaffected individual does, and this is more than enough to prevent the onset of disease. There are likely other molecular mechanisms involved to express the functional version even more, so their levels may be even higher than 50%.

So, while there is certainly a strong negative selection pressure on people carrying two copies of a mutated allele (or two different mutations, there are actually many of them) that prevent most or all expression of active protein, that same selection pressure does not apply to heterozygotes, and so the mutant alleles remain present in the population.

I strongly recommend reading through the fairly short but definitely thorough course Understanding Evolution from the University of California, Berkeley. It may explain some of the concepts I've mentioned more clearly.

Note: I once worked for Shire, which, among other things, specializes in rare diseases including lysosomal storage disorders. I specifically worked with their Hunter Syndrome therapeutic, known as Elaprase. Other companies are also working on various therapeutics.

This is in no way an endorsement of the company or its products, it's just where I learned all of this stuff.


Are all mutagens carcinogens? Not all carcinogens are mutagens. Alcohol and estrogen, for example, does not damage DNA.

It's one of the assumptions of the Ames test that mutagenicity implies carcinogenicity, but is this always the case? I assumed that it was, but then I saw one of the comments here. I did some more research but the internet seems to be reluctant to be definitive on the subject. This guy claims 'no', but I'd prefer sources or at least a response that handles counterexamples like HPV. This paper claims 'yes', but doesn't list any specific examples. Some mutagens might be more specific to genes involved in cell cycle regulation, so I could see how a weak mutagen is a powerful carcinogen.

My question is, can you go the other way? Are there mutagens that just do not cause cancer? If they do not exist or are not known to exist, are they even possible?

Short answer
All mutagens are potential carcinogens unless the mutagen is highly specific to a site. As noted in the question, carcinogens need not be mutagenic.

HPV causes oncogenic transformation of a cell because of certain proteins that it expresses. HPV is considered a carcinogen by the IARC. Some retroviruses are oncogenic: they might carry an oncogene or insert randomly near an endogenous proto-oncogene and cause oncogenic transformation; this phenomenon is called insertional mutagenesis (Coffin JM, Hughes SH, Varmus HE, editors. Retroviruses). They can also integrate within a gene and knock it out. Many of these viruses are considered carcinogens by IARC.
Hepatitis viruses (B & C) can also induce carcinogenesis but insertional mutagenesis is not the sole mechanism (Cougot et al., 2005; Fung et al., 2009; Lemon & McGivern, 2012). Hepatitis viruses are considered carcinogens by IARC.
Ethanol in alcoholic beverages is considered carcinogenic by IARC. There are many substances listed as carcinogens by IARC but they are not mutagenic. The general mechanism of carcinogenesis by these substances may be prolonged inflammation or ROS generation.
Loss of function of the tumour suppressor gene p53 leads to cancerous progression (Chiche et al., 2016; Venkatachalam et al. ISBN:978-1-59259-100-8). So an siRNA that targets p53 should be called a carcinogen. It would however not cause any mutations and is hence not a mutagen.
If you consider the tools developed for genome editing, such as ZFN, CRISPR-Cas and TALEN as mutagens then they are not carcinogenic. However the term mutagen is not used for these molecules. Mutagen almost always refers to a molecule that causes random mutagenesis thereby making it a potential carcinogen.


Is "aggregate percentage" still a valid term in ecology? Martin et al. 1946 define "aggregate percentage" as a metric that describes the mean percentage contribution of a group to the total mass/abundance of all samples. The metric is useful in datasets that are plagued by outliers and non-normality, something that is a commonplace with most ecological community and diet studies in my experience. Aggregate percentage is calculated as follows:

$AP_i = \frac{100\%}{N_y} \times \sum\limits_{j = 1}^{N}(\frac{a_{ij}}{\sum a_j})$

Where i is the i$^{th}$ taxon, j the j$^{th}$ sample, N total number of samples, a$_{ij}$ the abundance or mass of i$^{th}$ taxon in j$^{th}$ sample, and $\sum a_j$ the summed abundance or mass of all taxa in j$^{th}$ sample.

Martin et al. 1946 illustrate this as follows:

I am sure that "aggregate percentage" is a standard method in ecology, but I cannot find many studies using this term by googling. Probably the method has synonyms and there might be a more accepted term for the method nowadays. My question is what is the valid term to use for the method?

The formula of "aggregate percentage" that you show is just the arithmetic mean of percentages, and I suspect that no special term is used in most studies that use mean percentages as a measure of e.g. prey composition in a certain predator (as seems to be the case in your example).

When searching for studies I think you will have more luck with using "mean prey percentages", "prey percentages" or "mean percentage composition". For instance, see Shoup & Lane (2015) which includes the text (with my emphasis):

  Results of regressions correlating Secchi depth (mm) with prey percentages by weight in the stomach contents of Largemouth Bass sampled from Boomer.

Also (Ahlbeck et al, 2012):

  For each of the 25 individuals in each size class, the diet composition was calculated as the mass percentages of different prey, and then the average mass percentages were calculated for the size class.
  [...]
  prey percentages were first calculated for each fish separately and then averaged over all individuals in the sample (Hyslop 1980).

Finally, Ledger & Hildrew (2008):

  Mean percentage composition (food category area as percentage total particle area) of faecal pellets of N. pictetii nymphs fed biofilm from four acid streams and four circumneutral streams.


What if we blend hydras to form a soup. will they still regenerate to form new individuals? Hydras can regenerate if cut into pieces. But if we take a pound of alive hydras in a blender/grinder and blend/grind them to form a jelly like liquid made of hydras where we have finely blended them, then will this soup turn into millions of hydras or they will die and rot

Based on this article, the answer is probably no. Quote (emphasis mine):

Small tissue pieces were excised from wild-type polyps of Hydra magnipapillata, allowed to regenerate, and the size-dependent characteristics of head regeneration were examined. The excised tissue piece was initially a square flat sheet. This piece gradually rounded up and, within 24 hr after excision, turned into a "spherical shell" which had a continuous ectodermal layer outside, a continuous endodermal layer inside, and an empty cavity at the center.
The smallest spherical shell that could be produced had a diameter of 0.2 mm and contained 270-300 epithelial cells. A tissue piece too small to form a spherical shell always disintegrated, presumably due to lack of an osmotic harrier between the tissue and the environment.

In short: any piece of hydra tissue with a diameter less than 0.2mm or that contains less than 270-300 whole epithelial (skin) cells is incapable of surviving and regenerating. It is highly unlikely that any hydras would survive being blended because the pieces would probably be too small or too damaged to be viable. Of course, if you had a chopping machine that cut hydras into large enough pieces without causing any significant cell damage, you could probably manage to create a large number of hydras in a very short time span. (I'm not sure why you would want to, though.)


Do you have experience with PacBio? I prepare a experiment and I found $PacBio SMRT$ as the great way to sequence my PCR products. I find the cost: library preparation 655 dollars + sequencing 435 dollars. It seems very low. Do you have some experience how much of sample can I sequence in one run (by coverage around 30) and if it is really for this price?

If it is a good idea to use PacBio depends a lot on what you want to sequence and what you want to do with the data you get. In short: you get longer reads but about 15% error per base. This means, you will have to cope with those errors, there are possibilities to do that. How much coverage you will get of you sample I cannot tell you, as I do not know what kind of sample you want to sequence.

How much data you get out of one SMRTcell depends also on the chemistry, I think it currently is between 275 Mb and 375 Mb, depending on chemistry. They have a nice brochure you could look at.

Anyway, you probably will have to get some advice by a bioinformatician of you choice on how to design and analyse your sequencing experiment.


What is the connectivity between on-center & off-center bipolar cells? Do rod-photoreceptors only form synapses with on-center bipolar cells (and on-center ganglion cells in the next step)? If so, why is that?
Why do rod-cells only connect to on-center cells, while the cones connect to both on- and off?
Am I correct in saying that what happens in the bipolar cell as a response to light stimulus on a photoreceptor depends on i) Wether it is an on-center or off-center bipolar cell - and of course where the light stimuli is focused on the bipolar cell (periphery or center), or ii) What kind of receptors the on-center and off-center bipolar cells have? This is the part where I get really confused, because I read somewhere that what kind of receptors On/Off-center bipolar cell have, is not something set in stone? So saying that On-center bipolar cells have AMPA receptors and will, as a result of that, react in a specific way to less Glutamat release would be wrong?
How does this release of neurotransmitter works together with central / periphery stimuli. Let me try and use an example, You have an on-center bipolar cell. What will happen if light is focused on the center of this cell's receptive field? And what will happen if it is focused on the periphery? Let's just say that the light hitting the center of this cell's receptive field causes it to be depolarized. But is it really the light hitting the center which causes this effect, or is it the decrease in Glutamate release from the photoreceptor that causes this effect? If the latter, then what does it really matter if the light hits the periphery or the center of the bipolar cell's receptive field? The photoreceptor is hyperpolarized by light either way and less Glutamate will be released no matter what.
Also, in order for this to make sense, the light that enters the eye is absorbed by the photoreceptors pigmentmolecules, but some of the light also has to hit the receptive field of the bipolar cell in order to decide which signal to be transmitted? So not all of the light is absorbed by the photoreceptors then?
If the light hits the periphery of an On-center bipolar cell, you will have an inhibitory effect, is that right? And the other way around, if the light hits the center of the cells receptive field, you will get an excitatory effect? But I am curious as to how this also has to do with the kind of receptor that the on-center bipolar cell has (AMPA or MGluR6).

First off, the post is quite lengthy and contains various sub-questions. I will answer the first two questions in detail, but only after starting with an abstracted overview of photoreception in the retina. By the looks of it, your basic understanding of photoreceptors and secondary visual neurons is incorrect. Clearing the general neurophysiological workings of the retina up should get you on your way in understanding questions 3 - 6.

Synopsis of information flow in the retina: sensation of light
In Fig. 1 a schematic of the retina is shown. It basically consists of three layers. Layer one contains the photoreceptors, namely the rods and the cones. These primary sensory neurons absorb the light with photopigments and generate electrical signals in response to that. The photoreceptors, in turn connect to the second layer, namely bipolar cels, horizontal cells and amacrine cells. These cells are responsible for the center-surround structure of the receptive field of the last layer of cells (Fig. 2), namely the retinal ganglion cells in the front of the retina, whose axons pass across the surface of the retina and form the optic nerve (Kolb, 2017).

Fig. 1. Retina. source: Quasar Group

Note that there are no light-sensitive cells in the retina besides the rods and cones (barred the retinal melanopsin ganglion cells, but please forget that for the sake of simplicity). This one detail should basically clarify the sub-questions 3 - 6 in your post. The first two questions I will address next.

Fig. 2. ON and OFF center responses. source: McGill University

Regarding the retinal bipolar system and your first two questions:

  Do rod-photoreceptors only form synapses with on-center bipolar cells (and on-center ganglion cells in the next step)?
  and
  Why do rod-cells only connect to on-center cells, while the cones connect to both on- and off?

Rod bipolar cells in the mammalian retina are of the ON type. In contrast to the cone system, rod bipolar cell signals are split into ON and OFF components by amacrine cells. The cone system piggybacks then on the cone system; Rod ON signals flow from rod bipolars to amacrine cells to ON cone bipolar cells. Rod OFF signals are generated between amacrine cells and OFF cone bipolar cells (Nelson & Connaughton, 2017). See Fig. 3 for an overview of the retinal connectivity between rod and cone bipolar cells.

Fig. 3. Retinal circuitry. source: Nelson & Connaughton (2017)

References
- Gouras, Color Vision: In: Webvision: The Organization of the Retina and Visual System (2017)
- Kolb, Simple Anatomy of the Retina. n: Webvision: The Organization of the Retina and Visual System (2017)
- Nelson & Connaughton, Bipolar Cell Pathways. In: Webvision: The Organization of the Retina and Visual System (2017)


Any examples of an organism's life cycle where the reproductive stage occur before the 'adult' stage? Most life cycles we knew of consist of a juvenile stage (e.g. larval for insects, sporozoite for some intracellular parasites), a reproductive stage and an adult stage. Usually the reproductive stage occur when the organism reached the adult stage.

But are their examples of organisms where its natural life cycle involve reproduction at an early stage, and then the parent then went through more distinctive stages after the reproductive stage and then dies off? For example:

The closest thing I can think of is the life cycle of mayflies, which dies a short period after the mating stage. But mayflies has only one adult stage thus it is does not really answer the question

There are two important points here:

The adult phase is defined as the phase during which reproduction occurs. It is therefore impossible for reproduction not to occur during the adult phase as you would immediately call this phase the adult phase. Because of this purely semantic issue (nothing to do with biology) the answer to your question is necessarily "no".
Only kin selection/group selection/lineage selection makes life after the reproductive age possible. It is therefore a pretty rare phenomenon. If this is unclear, you may want to read things about the evolution of ageing such as this post for example.

Maybe a question that would be of higher interest would be something along the lines of: "Can you list species that have non/reproductive phases in between a reproductive phase and death?" or "Are there any species that undergo different reproductive phases during their lives such as being first a sneaker and then territorial (yes) or such reproducing asexually at first and then sexually (probably but can't think of any examples)?".


From DNA data, is it easier to conclude that chimpanzees are our close relative, than it is to do a paternity testing? Well, today I was contemplating on how to explain evolution, approaching with the dialectic method. When it came to why chimpanzees and us being so close in the tree of evolution isn't outright absurd, I formulated a witticism, "Well, today a glance at humans' and chimpanzees' DNA would confirm how much close we are. Compared to that, if you were to do a DNA paternity testing, you would have to do a bit more grunt work in that you would have to look for more nitty-gritty details that separate (and make similar) one human from another. So, ours and chimpanzees' closeness would actually be easier to conclude than to tell your parents apart from non-parents."

Well, was I correct? That this would be easier than that?

The answer is complicated. In the early days of molecular phylogenetics, it was extremely difficult to demonstrate whether chimps or gorillas are our closest relatives. This is because the common ancestor of chimps and humans lived between 5 and 8 million years ago, and the common ancestor of gorillas and humans (and chimps) lived around the same time, just a little older. This means that there was a rapid split of three lineages, and it was difficult to disentangle them. As molecular phylogenetics advanced, we could generate larger datasets, and it because clear that chimps and humans were sister taxa. The smoking gun that demonstrated that chimps and gorillas were not one another's closest relatives was found when sequencing across the chromosome region in humans that corresponds to where two of our ape ancestors chromosomes merged. Orangutans, Chimps and Gorillas have 24 pairs of chromosomes, humans have 23. Sequencing across this region shows the exact splice site, which can be associated with the same regions on two chimp or gorilla chromosomes.
To answer your specific question, if you sequence any two genes between chimps and humans, you will find that the sequences are almost identical, with perhaps 1 in 100 nucleotides being different. If you sequenced a human and a gibbon for the same gene, you would find more differences. But finding that the sequences are similar is not the same as finding relationship, which requires sequencing multiple genes from multiple animals. For example, some genes between humans and rabbits would be extremely similar. So inference of relationships takes a lot of data from a lot of different animals. As for paternity testing, these practical tests are based on a different technology, targeting many DNA repeat regions or single nucleotide polymorphisms at specific sites that vary among human populations. But since the test is prescribed, and established, they are cheap, quick, and easy.


Beetroot white skin mould Does a mould make a beetroot poisonous or inedible ?

Lemon's mould for instance, makes penicillin, but it's green there, and I'm allergic to penicillin, would the white mould produce penicillin too?

From a study titled "Production of Penicillin by Fungi Growing on Food Products: Identification of a Complete Penicillin Gene Cluster in Penicillium griseofulvum and a Truncated Cluster in Penicillium verrucosum", moulds on food items were analyzed for fungi that could produce penicillin. The conclusion drawn was

  Among different fungal species belonging to the genus Penicillium that
  are currently used as starter cultures in the food industry or that
  are frequently isolated from cured meat products, only P. griseofulvum
  (in addition to the previously reported P. chrysogenum and P.
  nalgiovense) was found to produce penicillin and possess the three
  penicillin biosynthetic genes (pcbAB, pcbC, and penDE).

Even penicillin should be avoided as the paper states that

  The presence of penicillin in food must be avoided, since it can lead
  to allergic reactions and the arising of penicillin resistance in
  human-pathogenic bacteria.

During world war two, a strain of Penicillium chrysogenum was isolated from the mould growing on a cantaloupe (reference) for the development of penicillin. This was after searching through many mould families developing on different food items so penicillin strains do develop but are rare.

The problem faced is that moulds cannot be differentiated from each other through sight nor is all penicillin moulds safe (reference). Whatever be the case, I hope that you didn't venture to try and eat that beetroot.


How to retrieve logical expression (KO based) for reactions from KEGG? Whether a module is complete or not can easily be checked by evaluating the Definition entry associated with the module; e.g. in module M00010, it is given by

Definition  K01647 (K01681,K01682) (K00031,K00030)

which can be translated to

K01647 AND (K01681 OR K01682) AND (K00031 OR K00030)

If this expression evaluates to TRUE, the module is complete.

Now I am wondering whether analogue information exists for a single reaction. So e.g. for R00352, one finds the following information about Orthology:

But how do I now know in which logical relation the KOs are?

So it could be

K01648 AND K15230 AND K15231

or

K01648 OR (K15230 AND K15231)

and so on.

Can this information be retrieved from KEGG and if so, how?

EDIT:

In the above example, the correct expression would be:

K01648 OR (K15230 AND K15231)

One either needs K01648 or the other two subunits together. So, unfortunately, it is not as easy as @aretaon describes it in his answer since just one of the two subunits would not be sufficient. One can therefore not just connect the KOs associated to a reaction using a logical OR.

To rephrase what you already mentioned in your question: For a KEGG Module to be completed (so that an organism can perform a certain function) you need a certain set of functional units or enzymes. So to evaluate the abilities of an organism you would check its genome for the gene sequences related to the module by performing the logical operation you mentioned above.

A Module is composed of chemicals (C) and reactions (R), as you can see in your given example. To explain the differences between modules and reactions best have a look at the last reaction, Isocitrate to 2-Oxoglutarate. There are three boxed reactions (one of them is a combination of two) that all lead to Oxoglutarate. When you look at the Orthology (the enzymes involved) for the reactions in the first box (R01899+R00268) and the second box (R00267) you will see, that it's the same enzyme (K0030) performing different reactions. The third box now contains a reaction (R00709) performed by a second enzyme (K0031), that leads the same way (it differs in using NAD+ instead of NADP+ as electron acceptor). So for the module to be completed you could use either of the two (that’s the reason for the OR-operator in the logical operation).

If you now want to evaluate if a certain type of reaction occurs in a given organism it is sufficient to have one of the possible enzymes catalysing this reaction. So:

K01648 OR K15230 OR K15231


why do some cells in the body prefer necrosis to apoptosis as a means of cell death? There are many programmed cell death pathways, but some cells show a greater preference for some over the other. I'm wondering as to why if necrosis is an inflammatory response that causes damage to neighboring cells, why some cells would prefer this as opposed to a more controlled mechanism such as apoptosis or even autophagy.

There is actually no preference for apoptosis or necrosis in cells of the human body - both types can occur in all cells and they have different triggers. The main differences can be seen in this figure (from here):

Apoptosis (also called programmed cell death) has three different triggers (intrinsic, extrinsic and Perforin/Granzyme pathways), see the image below for details (from reference 1):

All three activate different components and caspases in the beginning but finally all activate Caspase 3, which finally activates endonucleases (which degrade the chromosomal DNA), Proteases (which degrade the proteins in the nucleus and the cytoskeleton) which leads to the degradation of the cell. In the end apoptotic bodies are formed from the cell. Additionally the mitochondria break down and release cytochrome c and ATP. Their release from the cell attracts macrophages which take up and eliminate the apoptotic bodies and in turn release cytokines which suppress an inflammatory response.

Apoptosis goes on in a ordered way and does not trigger any further reactions in neighbouring cells (except these receive the same signal). See also reference 1 and 2 for more details.

Necrosis is triggered by external stimuli of the cell as injury of tissues or toxins from infections. Necrotic cells swell, while there internal structures are in a state of unregulated degradation. Finally the membrane will burst and set free cytochrome c and phosphatidylserines from the membranes which cause inflammation in the affected tissue. The necrotic cells are not removed by macrophages which allows the released interior of the cell to spread further and cause problems.  See reference 2 and 3 for more details.

Necrosis is usually not as a beneficial process, but there are also publications which see
the process as a specific form of cell death (see reference 4).

References:

Apoptosis: A Review of Programmed Cell Death
Apoptosis vs. Necrosis
Cell death by necrosis: towards a molecular definition
Review Necrosis: a specific form of programmed cell death?


Reusing frozen blood Considering the short supplies of blood in hospitals, why can't we freeze on our blood from time to time and and have it stocked for reuse in an emergency?
That could make ourselves responsible for own our blood supply in case of an emergency.

Freezing cells is difficult, almost an art form. It depends largely on the types of cells being frozen, the program to be used in freezing and the program used to thaw. You can end up with a massive loss in viability if a technician doesn't follow a freeze or thaw protocol to a tee, and there are release criteria where products of low viability cannot and should not be infused.

Being said, cryopreservation of blood for transfusion exists, and has since the Vietnam war. We're getting better at the process, but barriers such as cost and training probably still pose a hindrance.

Another barrier is maintenance of stocks, especially if you're considering monitoring your own blood supply. A cryogenic freezer would need to be maintained and monitored for constant -160-170°C. Cells do not undergo multiple freeze-thaws and thus once thawed you have a short shelf life.


Electrocardiogram: Difference between Atrial Fibrillation and Atrial Flutter I have been working on analyzing Electrocardiogram data.

I have read several documents related to conditions of the Atria during fibrillation and flutter, the most lucid being that atria quiver with rapid rate.

This manifests as multiple P-waves (some documentation refers to them as "F-waves" and regards P-waves as absent) in the Electrocardiogram.
However in this condition, we get a completed QRS-complex in the Electrocardiogram.

Now, coming to my question, in both scenarios i.e. Atrial Flutter and Atrial Fibrillation, i get multiple P-waves(or F-waves) with completed QRS.
So how do i differentiate between the two conditions ??

A-Flutter will have discernible waves that can be counted, usually. The R-R interval will be regular or maybe slightly irregular if there's a variable conduction block in the AV Node. A-Fib will ALWAYS be completely irregular without discernible pattern.

You can also modify the position of your limb leads. There is an EKG placement called the S5-Lead that basically makes it where the QRS disappears because it's electrical impulse is perpendicular to the monitoring leads. The Atria however, become super-visible on the EKG.

To do S5:
Place the RA electrode on the patient's manubrium.
Place the LA electrode on the 5th intercostal space, right sternal border.
Place the LL electrode on the right lower costal margin.

Then set the EKG to view Lead I


IPTG and lac operator with e coli for foreign gene question We did an experiment were we have e coli with a plasmid with a gene from another bacteria in it, and we put in IPTG in for induction. Will after looking up more about IPTG online I see it's related to the lac operator, which from what I've found just deals with lactose. Is there some other function that has? How can this be related to or effect the thing we put in and what we're doing? I'm missing the connection here.

The lac operon contains genes which are important for the metabolization of lactose as an energy source - normally glucose is used for this purpose. Usually the operon is tighly regulated and as long as there is another source of energy it is kept in an inhibited state.

The presence of lactose removes the lac repressor from the lac operon and allows the expression of the genes and thus allowing the metabolization of lactose. The mechanism can be turned on and off depending on the presence of lactose.

IPTG is a substance which mimicks the presence of allolactose (a metabolite of lactose) and it can activate transcription from the lac operon. As IPTG (in contrast to allolactose) cannot be hydrolyzed by β-galactosidase, it's concentration in the cell stays the same. Using the lac operon and IPTG enables you to switch on the expression of the gene on your plasmid and to start the overexpression.


Can animals that rely heavily on sonar sense colour? Apparently there're species around as rely heavily on sonar to sense the world around them.

E.g. Bat, Dolphin, Whale ...

The humans, and other terrestrial beings in a lighted world are capable of distinguishing colour in varying degrees of acuity. Is this ability to sense colour in our environment applicable to species (terrestrial, avian, and marine) that rely heavily on sonar?

Any animal using sound cannot sense color though sonar directly, though these animals are not entirely blind and can probably see colors in the infrared we can't.

  Even on the darkest night there is some light around and all bats use this. Old World fruit bats have colour vision, which is useful to them as they are often quite active in daytime, roosting on trees in exposed positions, rather than tucked away in dark crevices like most microbats, which can see only in black-and-white.

Dolphins have additional senses in addition to seeing they can sense electrical fields.  So if an animal has its eyes covered, they will seem to be able to do things you would not expect.  Its not the same as seeing the color though.

Such animals using sonar can additionally sense density and hardness as well as other material attributes which would cause the acoustic properties of the material as well as movement.

  A hard-bodied insect produces a different quality of echo from one with a soft body, so bats can distinguish between some different groups of insects in this way. They can also determine the size of the object.

What's really interesting is that even human beings can experience this unusual sense.  Blind people have learned to echolocate by making clicks with their mouth, and there is a movement to teach this skill.

Anyone can try it.  In just an hour or two I was able to tell how close I was to a wall, whether the wall was concrete.  I couldn't play video games (2:20 on the link) or see colors though.


Can you identify this snake? On a walk through I’ON Swamp/Natural Forest in Mt. Pleasant, SC, we came upon this snake. We did not get too close for fear it may be poisonous.

It had a very dark brown/taupe exterior with almost a diamond shaped head. It had a reddish, orange belly. It was ~3-4’ in length and fairly large girth.

Hard to tell without a clearer picture, but the size and color pattern seem to match the description for the Plain-bellied Watersnake.
See for example the following picture from the Virginia Herpetological Society:

I assume from the location being in something called a swamp that the habitat (in and near slow moving bodies of water) also fits.


Can you identify this insect? I found this insect in my own courtyard in the city of Pamplona, Navarre, Spain; during mid-February. My courtyard is never directly exposed to sunlight and is always cold, poorly lit and humid. It was 15 millimeters (0.6 inches) long when it kept its body still and straight, without counting the antennae which were 3 millimeters long each (0.1 inches). Its abdomen covered 2/3rds of its body length, and it constantly curled up and down. It also had a pair of wings, with the beginning of each partially covered by a shorter, brown, wing-like structure. To the exception of those brown coverings, its entire body was jet black and was slightly shiny.

I kept it in a test tube and put it with a spider that was almost its size. It was undisturbed by the spider and even approached it often.

Update: It dismembered the spider in less than a day.

It is a rove beetle (Coleoptera, family Staphilinidae). These are among the most specious of beetles. You can recognize them because the elytra (forwings) are much shorter than the abdomen.https://en.wikipedia.org/wiki/Rove_beetle


Human bone density and Brown Bear bone density? It is stated on this website that the density of a Grizzly bear bone is ten times our own. And since I am not into biology at all, I am confused as I don't understand the meaning of bone density here.

I know what the "bone mineral density" term means, and I know it is measured in $g/cm^2$, but there is also the "physical" density term which is the mass by volume and it's measured in $g/cm^3$.

Now, what does it mean when we say that an animal has a bone that is 10 times more dense than ours ? Does it mean that the bone weighs 10 times more for the same size (or volume) ? Or does it mean that it has 10 times the amount of minerals and so it is somehow stronger ?

The word density in the medical term bone density is used to quantify only the mineral content of the bone (bone mineral). It's not intended to describe the total mass density of the bone like we are used to from physics.
This is all on wikipedia: http://en.wikipedia.org/wiki/Bone_density
Thus, when one say that a Grizzly bear have 10 times the bone density, it implies that its bones have 10 times the mineral content compared to humans, and this is indeed seen as a proxy indicator for bone strength. However, this claim does seem unsupported and unrealistic as kmm points out.


Do thymine and uracil ever appear in the same strand of RNA? Wikipedia says that "in RNA, thymine is replaced with uracil in most cases."  I'm curious what are the cases when this does not happen?  Does this ever occur in normal functioning, or is it an error?  Do T and U ever appear in the same strands of RNA together, or does a single strand just use T or just use U?

tRNA molecules contain a T in the T arm. I believe that this results from post-transcriptional modification of a U by uridine methylase.


Why is the floral biodiversity of grazed grassland higher than that of mown grassland? I have collected some data to compare the biodiversity of a field in which the plagioclimax is maintained by machine mowing with a field in which the plagioclimax is maintained by sheep grazing.

What I found was that there was a significant increase in floral biodiversity in the field which was managed by agricultural grazing when compared to the floral biodiversity of the machine-mown field.

I am trying to explain my findings, and I believe that it is due to the comparitively short amount of time that machine-mowing has been a grassland management technique, so there has been little time for natural selection to take place and for species to develop adaptations to machine-mowing (such as being low-lying, or extremely fast-growing). Whereas the field which is managed through sheep-grazing, contains multiple competing species which have adapted over time to grazing sheep, such as Cirsium arvense.

Moreover, the field which is managed by grazing has nutrients returned to it through defecation of the grazing animals, allowing for more favourable conditions for growth.

Is my explanation valid? Are there any other reasons why the floral biodiversity of a field managed by sheep grazing would be higher than one managed by machine-mowing?

Thanks in advance!

I think you may have covered the answer in your question... but here's my take;

The 'mowing' occurs at a distinct time-point and is highly destructive and uniform, so the selection pressure is very high and only highly competitive species that are fast to grow and reproduce will be successful.

As you point out, animals will defecate and naturally fertilize the land, thus favouring growth. Other favourable factors in an agricultural environment will be that the 'mowing' will be much less uniform; the animals may favour one plant over another - so a plant that is not eaten by the animals will continue to grow and reproduce, whereas in the mowing environment this plant would not succeed; this will allow various other species to succeed where they would not in the mown environment. Also, depending how many animals are in the area the height of the grass may be higher overall, so slower-growing plants could grow enough to reproduce.


How to measure trajectory regularity? I have two animal running trajectories. A regular one with repeated back and forth running between point A and B, like the one on top in the figure. The other one is very irregular, animal paused and turned around a lot in the middle. Is there any algorithm to measure the regularity of a trajectory, like repeated activity on the top? And compare the extend of regularity between the two trajectories? Thanks in advance.

In the world of physics, you can distinguish between random motion (e.g. thermal Brownian walk) and directed motion (called ballistic: think of a cannon ball) by studying the mean square displacement of the object: you'll be able to fit this displacement as a function of time by a linear law if it is random, and by a quadratic one if it is directed. Exponents in between will give you an indication of the degree of randomness. The advantage of this (even if it is not specialized for your case) is that there's a large body of work using this, including for living organisms.

Note also that if your motion is as in the first case above, you'll have ballistic motion for times smaller than the travel time from left to right, and diffusive (random) for times larger than that. This has been used e.g. to analyse the run-and-tumble motion of bacteria who have a short-time ballistic motion and then after some time tumble to explore another randomly-chosen direction.

Example of this type of coexistence of two regimes:

In the field of biophysics, much of this was initiated by Howard Berg and coworkers

In your first case, you'll have an initial ballistic regime and then something that plateaus (because you stay between A and B). The transition time-lag will be the travel time between A and B.

In your second case, you'll be able to characterize the random walk: if the animal is aiming at going from A to B but randomly errs for short times, you'll have a short-time diffusive behaviour, and an intermediate time ballistic one. (And then again a plateau, as in the first case and for the same reasons). If the animal reaches B by mere chance, on the contrary, you'll have a diffusive regime only before this plateau.


How do animals decide what to eat and what not? I want to know this in particular about animals that no longer eat what they used to eat. The best example in my opinion are chickens. Chickens are often held to eat all kinds of food we would otherwise throw away. Most of this, they would never find in nature.
Chickens almost eat everything, but there are things they don't. Also, they often have a clear preference for some food.

How can they differentiate this food? Do they use smell? Looks? How can they know smells of food they never had before?

To answer with a question: How do you decide what to eat (if you don't know whether something is edible)?

All animals have evolved taste and smell (and I'm sure even prior to eyesight). The purpose of taste and smell in terms of nutrition is to determine if something is edible. If something tastes bitter or extremely sour, this is mostly a warning sign for toxins or advanced microbial degradation. The same accounts for smell: If you let raw meat foul, the smell is unbearable. Why? Because our brain is telling us not to eat this.


How long do fishes survive in a milk environment? Suppose you placed a fish, a goldfish for example, into milk instead of water. How long could you expect the fish to survive?

Would it die due to lack of oxygen? Is there any other factor that could cause the death?

I can't support this answer with scholarly articles. But it's an interesting question if you think of milk as highly polluted water.

Water from a tap (which is what goldfish usually live in) is 'fairly pure', with the naturally occurring minerals sodium, calcium, magnesium and potassium respectively in highest concentrations (varies by location.)

Milk, on the other hand, has not only a much higher mineral content, but also has fat, protein, carbohydrates, and white blood cells as 'pollutants'. In fact, whole cow's milk is only ~87.8% water.

Looking at calcium alone, the concentration of Ca in water is about  3 mg per 100cc, or .003%. Milk has .13% Ca, or 130 mg per 100cc. Since Ca is a major player in nerve and muscle function (in humans, a very relatively mild increase in serum Ca causes tetanic contraction of muscle), my guess is that the poor little fish would not be able to maintain normal serum Ca levels for long. It would die of inability to move fluid over its gills, that is, it would suffocate even in the presence of dissolved oxygen. Not to mention that the gills would also be coated to some extent by fat (3.5%), protein (3.8%) and other 'gunk'.

How long would it last? Probably not more than a few minutes.


If DNA has a half life of about 500 years, how can old seeds be planted? According to this article, DNA has a half life of 512 years

Wikipedia claims that there are seeds planted as old as 31000 years

Doing the basic math $100 / (2^{30000/512})$ we get that only about
$2.2989191*10^{-16}%$ of the DNA would be left

So how do these plants still grow when replanted?

That half-life was for temperatures of 13.1ºC. In more ideal conditions, such as for temperature of −5 ºC or drier conditions, the half-life would be longer. The Wikpedia article in fact states that the seeds that were 31,000 years old were frozen under permafrost.

The original article estimates that the half-life at −5 ºC (for a 30 bp fragment of mtDNA from bone) would be 158,000 years. I'm not sure how well this data can be extrapolated to seeds.


Difference between the P4 and P5 subtypes of P-type ATPases in plants In plants there are various kinds of P-type ATPases. What is difference between P4-ATPase and P5-ATPase?

There are numerous differences between the various subtypes of P-type ATPases, simply because they have different amino acid sequences. Three important differences between P4 and P5 subtypes of P-type ATPases are the following:

Structurally, P4 ATPases have their supporting structural domain (S) in the C-terminus, while P5 ATPases have the S domain divided over the N and C termini. Figure 1 shows the basic structure of P-type ATPases.
Structurally, P4-ATPAses require a beta-subunit for proper function (Poulsen et al., 2008). As the substrate for P5-ATPases is unknown, it could not yet be tested if they also require a beta-subunit.
Functionally, P4-ATPases are putative lipid flippases, while P5-ATPase pumps have so far (per the 2011 report cited) no assigned substrate specificity.

Schematic outline of P-type ATPases. Source: Palmgren & Poul Nissen (2011)

References
- Palmgren & Poul Nissen, Annu Rev Biophys (2011); 40: 243–66
- Poulsen et al., Plant Cell (2008); 20: 658–76


The falsifiability of natural selection I was wondering if we could think about experiments to falsify natural selection . According to this wiki : we could invalidate natural selection

  “...if it could be shown that selection or environmental pressures do not
  favor the reproductive success of better adapted individuals”.

So, to test this hypothesis we would have to:

Have different individuals that are defined as more or less adapted to a given environment
Put them in that environment
See if the better adapted individuals have a better reproductive success. (I will avoid the word fitness because one can consider it already contains the principle of natural selection)

But is it possible to define a priori that an individual is more or less adapted? Of course, we could suppose a priori that because of some or other trait (higher longevity, higher stress tolerance, or whatever), an individual carrying that trait will be more adapted. But if we find out this individual does not have a better reproductive success in that environment, we could conclude it was just not the right trait to be better adapted and it would not invalidate natural selection.

Isn’t it, on the contrary, the fact that some individuals have a better reproductive success which allows defining them as better adapted a posteriori? There would then be some kind of a vicious circle.

Ok, so one could say that we do not need to define a priori better or less adapted individuals. We could just put individuals in an environment and see if at least some have a better reproductive success. That would mean that they are better adapted –and so that natural selection occurs-. But suppose we find no significant differences in individuals reproductive success: that could indeed mean that natural selection does not exist. But, well, that could also just mean that there was no selection pressure in that environment.

So if we want to test natural selection existence, we need either to get individuals that are a 100% sure better adapted than others; or environmental conditions that 100% sure exert selection pressures on organisms ; and we need to know this a priori. But, it seems to me that considering an individual as “adapted” or an environment as “selective” can only be done a posteriori if we already accept the idea of natural selection.

That’s why, to me, it is difficult to think of an experiment that would falsify natural selection. Is natural selection falsifiable ?

What is natural selection?

Natural Selection (NS) is an evolutionary process causing a directional change in both a phenotypic trait and the allele frequencies associated with particular values of this phenotypic trait whenever there is a trait that

Has a non-zero narrow-sense heritability $h_N^2$

See this post for the definition of heritability
Note that if $h_N^2 ≠ 0$, then it necessarily implies that the trait is variable in the population.

Correlate with fitness variance in the population

See this wikipedia article for the definition of correlation

You may want to have a look at this post (maybe in particular Lewontin's recipe explained in this answer) or have a look at an intro course to evolution such as Understanding Evolution by UC Berkeley if this is unclear to you.

You may also want to have a look at the post How is “selection” best defined?

Note about the environment

Note that the genotype - fitness covariance does not necessarily need to be dependent or correlated with a specific environmental variable. Many selection pressures are indeed independent of the environment. If one specific genotype is associated to heart failure, then the environment may matter little. This genotype will always be associated with lower fitness.

In other words, you do not need environmental change, or environment specific adaptations in mind to test NS.

Would evidence that what is needed for natural selection to happen does not exist falsify NS?

Mutations

I don't think that an evidence that mutations do not occur would falsify NS because while NS needs genetic variation (fuelled by mutations), the process per say does not refer to the creation of new genetic variance via mutations. Showing that mutation do not occur would not per say falsify NS (I think) but it would make the point that NS cannot happen. A bit like, the absence of energy would not falsify the theory of gravity but it would prevents any gravity to ever happen.

The theory of evolution as whole would be falsified if one were to show mutations never occur (or occur at a much lower or much higher rate than currently observed) though.

Heritability

Similarly, if one could show that $h_N^2 = 0$ for all traits (nothing is heritable), then this would also prevent any NS to ever happen

Fitness variance

Similarly, if one could show that there is no fitness variance in population or even that fitness is always independent of the gentic variance (in other words, fitness itself is not heritable), then NS would never happen.

How to falsify natural selection?

You could show that for a phenotypic trait $h_N^2 > 0$ and show that genetic variance correlates with fitness variance (fitness can be measured as the number of offsprings) and yet repeatedly fail to see any change in the phenotypic trait values (or frequency of the loci explaining variance for this trait) over time. Such observations would falsify NS.


What is the mass of an E.coli cell? I'm trying to get into Biology, reading introductory texts. A discussion on E.Coli estimates the mass of the cell from $$density =1g/mL=1g/cm^3$$ and $$volume=1µm^3$$ From this I get $$ mass=density × volume = \frac {10^{-6} g}{10^{-2}}=10^{-4} g$$ which is wrong since the answer is supposed to be $1pg$. What am I doing wrong? Thanks!

Its simple:

Mass = Density * Volume

= 10^3 (Kg/m3) * (10^-18 m3)

= 10^-15 Kg

which is equal to 10^-12 gram or 1pico gram


Questions regarding serial passage of virus through animals arising from the paper The proximal origin of SARS-CoV-2 In this answer on bioinformatics.stackexchange.com to the question inquiring about the validity of the paper Kristian G. Andersen et al, The proximal origin of SARS-CoV-2, the author asserts the following two points, which I do not understand.

Serial passage of a virus through either animals will always attenuate the virulence, say the affinity to the ACE2 receptor, of the virus. My question: Could people artificially select for thus increase the virulence of the virus?
We can always tell whether a virus is artificially serially passed because we know the mutational patterns of other serially passed viruses. My question: How does this distinguish artificial from natural passage?

No. Serial passage through animals attenuate the virulence of a virus In It's ORIGINAL Host. it can cause and will cause an increased virulence in the animals that were used in serial passage, and, if the animals have similar receptors as humans, increase the virulence in humans as well. like the two experiments that passed bird flu across ferrets until they become virulent and airborne across them.
https://www.cidrap.umn.edu/news-perspective/2014/04/experiments-render-h7n1-virus-more-contagious-ferrets
https://www.scientificamerican.com/article/pandemic-bird-flu-studies-public/
https://science.sciencemag.org/content/336/6088/1534.full
https://jvi.asm.org/content/88/12/6623


Case study and speculations on the brain of Edward Mordake I am very interested in the case of the man named Edward Mordake who lived in the 19th century. In particular, he had two faces. If you have not heard of this man, please, search this up as there are a very few amount of photos, but it is something very, very strange.

However, all the information on him seems to be speculation, so I am looking for a scientific look at this. I am unsure if it will even be possible seeing as how the years have passed and records may not have been accurate.

To be specific, has this condition been noted before? There seems to possibly be differing opinions onto wether the face was indeed its own individual inside, or a low functioning other half of the same man.

Indeed I am looking for any info on the biology of his brain, possibly the neuroscience and or physiology, and of course any comments and discussion.

Thank you

Mordake was a conjoined twin fused at the head (Fig. 1). Twins conjoined at the heads are rare, occurring only once in every 2.5 million live births. Moreover, in Mordake's case it was a parasitic twin head with an undeveloped body that was fused with his own head. This condition is referred to as craniopagus parasiticus, or épicome / epicomus. Craniopagus parasiticus is an extremely rare teratology, of which only six cases have been recorded in the medical literature (Bondeson et al, 1989).

Fig. 1. Wax reproduction from Edward Mordakes face. Source: Bosmia et al., (2014).

The story of Edward Mordake is, however, obscure and met with skepticism. Moreover, no medical details are known as far as I know. However, he was reported to be intelligent and healthy, just depressed by the second parasitic head (Bosmia et al, 2014). To me it appears a story of a person with a normal brain and a parasitic face attached to his head. However, there are rumors that the parasitic head could talk independently, leaving open the possibility that the parasitic head may have contained a separate brain, or shared Mordake's own brain.

More is known about the double-headed Bengal of Everard Home (Fig. 2).

Fig. 2. Skull of the double-headed Bengal (museum exhibit, left) and an artist's impression of the case (right). Source: Bondeson et al, (1989)

The natural head and body were perfectly normally developed, but a number of anomalies were noted on an examination of the parasitic head, such as excessive tearing and the absence of pupil reflexes. Upon dissection the parasitic head was shown to show various anomalies, such as missing anatomical elements (e.g. auditory canal) or underdeveloped structures (e.g., small lower jaw bones).  Importantly, the brains were separate from each other and covered in individual and proper coverings. The dura mater of each brain adhered firmly and contained
many large vessels. Bondeson et al. (1989) describe the remainder of the six cases as well, which were still-borns or lived just very shortly. They had completely separated brains too.

References
- Bondeson et al, Surg Neurol (1989); 31:426-34
- Bosmia et al, Childs Nerv Syst (2014)


Help identifying a bug which looks like a housefly and mosquito hybrid I'm from Kochi, India (southern part of India). I found this bug inside my house , it was about a centimeter long . But how can such an hybrid be possible. (It was raining before I found it).
1: https://i.stack.imgur.com/Dlyio.jpg

This is a long-legged fly (Condylostylus spp).  Unfortunately your image is not sharp enough to give a specific species.  See this post of another Indian fly that is virtually identical to yours:
https://www.jungledragon.com/image/13762/long-legged_fly_-_condylostylus_spp.html


What is this small brown spider? Found in a doorway in eastern Tennessee. With its legs fully extended, it's about the size of a quarter.

This spider has a roughly globular abdomen, (actually kind of egg-shaped, and pointed, which is a good clue), and is hanging upside-down in a 3-dimensional web which (if we could see it) would look pretty tangled instead of a nice, 2-dimensional orbweb.  It doesn't have any noticeable pattern other than the banded legs, and the greyish-brown abdomen looks like it has some darker blotches.  It's made its web near the top of a doorway in a house.
These clues all point to a very common Theridiid spider which goes by the name of House Spider.  It's not the House Spider that spins a flat sheet from a funnel retreat - that's the Tegenaria House Spider.  This House Spider is the Theridiid House Spider Parasteatoda tepidariorum.  It's a harmless (to us) spider that eats almost anything it can entrap in its web.  I've seen them happily eat Gypsy Moth caterpillars, centipedes and other arthropods that aren't very popular choices among household spiders.
Here's a link that you can browse to see the wide degree of variation that this spider can show - but always a kind of smudgy, blotchy greyish brown abdomen, banded legs and the tangled web in which it hangs upside-down.  You'll note that the legs of this Theridiid, like most of its relatives, aren't as burly and sturdy-looking as those of its cousin the Black Widow.  These Theridiids kind of totter along on their relatively spindly legs when out of the web, while the Widows go striding along like small Mecha-Spiders.  I always expect to hear the Imperial March from Star Wars when I see a Widow walking on the floor.

https://bugguide.net/node/view/6919


Whitening of hair at old age Human beings have evolved from their ancestors to their modern forms adapting many changes in structure and I would assume that every change has a significance.

So, what is the cause of our hair turning white at old age? Was it meant for frightening away predators at old age when our body is weak? Or what is it actually?

It would be incorrect to assume that

  every change has a significance

from an evolutionary point of view. In many cases, the changes could be happening at an age where it does not affect it's selection, since it's past the reproductive age. This could certainly be true for greying of hair.

If you want to understand from the point of view of an evolutionary theory, there are at least two possible explanations. One is the Mutation Accumulation (MA) theory. It says that mutations causing late life deleterious effects can build up in the genome more than diseases that cause early life deleterious effects. This is for the simple reason that cases of the latter would be eliminated as they will usually affect in the reproductive period, but chances of a 60 year old grey-haired man to have offsprings is low. In essence, if a trait reduces survival in the post-reproduction period (which is the case here), then the effect of selection is weak for it. So, since grey hair arrive so late, they might not really be selected out.

Another is the Antagonistic Pleiotropy theory. Pleiotropy means a single gene having more than effect. So it says that if a gene improves fitness early on, but causes an undesired effect later in life, it will be selected for in the population. This is simply because the later deleterious effect does not affect the advantage the gene provides at the stage were reproduction happens. So, it is possible that the gene responsible for grey hair may also be making you more fit.

So, in summary, there seems to be no direct advantage of having grey hair. It could be the result of Mutation Accumulation, or the antagonistic pleitropy effects of the responsible gene.

You can read more about it in this and this answer.


Validated Protein-Protein interaction database for cancer I need to use validated PPI data in my research. Is there any database of such validated (like Mass Spectrometry) database for cancer?

One of the most popular databases of PPI data is STRING. It is not only for cancer though, but since many research is done in the field of cancer, you will find a lot of data derived from cancer research.


Do foods with preservatives become less toxic in the gut? Do foods with preservatives stay digestible for longer in the gut by not rotting as much (producing less toxins)?

Do foods with preservatives take longer to digest?

Food preservatives are either antimicrobials (e.g. sorbate, sulfite) or antioxidants (free radical scavengers such as butylated hydroxyanisole).

Digestion is initiated in the stomach by hydrochloric acid and pepsin. It continues in the small intestine with the action of numerous other enzymes including amylases, lipases and proteases. There is no obvious way that these digestive processes would be inhibited by preservatives.


What is meant by pro-acinar cell? What is meant by "pro-acinar cell" in the following sentence? progenitors/precursors?

A transient decline in Neurog3 expression from E11 to E12 coincides with peak segregation of MPCs into proximal, Ptf1aNkx6-1+ bipotent progenitors (BPs) and distal, Ptf1a+Nkx6-1 pro-acinar cells (PACs).

Thanks

'Pro-' is a general Latin preposition and English prefix with many meanings, but often in biology, as in this case, it means "before".  A proacinar cell is not yet an acinar cell (a cell of the acinus) but will be.  A related usage occurs with peptides such as proinsulin.
In Latin, "acinus" means a cluster of grapes.  You can find 'acini' in many places, notably exocrine glands, but in this case the pancreas is discussed.  With the help of Ms. Elbakyan, they tell quite a beautiful story, but the answer to this question is mostly in the first sentence of the abstract:  the stem cells (multipotent pancreatic progenitor cells) can become pro-acinar cells (which become secretory tissue of the acini, producing the pancreatic digestive enzymes), or else are reserved as bipotent progenitors that create the ducts and the islets of Langerhans.


Location of microbes causing eliminated diseases Do eliminated diseases like polio, smallpox etc still exist in locations they have been eliminated from or in the wild or did we just make them go extinct like the dodo?

Whether a disease can be eradicated or not depends on its reservoir. To be eliminated it needs to be eliminated in all places and organisms it can thrive in and spread from. This makes diseases like rabies for example hard to eradicate altogether because it can exist and spread in many different animal species.

Polio and smallpox however both have no non-human reservoir, which makes it possible to eradicate them. There is no "in the wild" for them to persist in because humans are "the wild" for them. So smallpox the disease has indeed been made extinct like the dodo; polio we're not quite there yet but we seem to be close.

I said "smallpox the disease" because "smallpox the virus" still exists in two laboratories in the US and Russia.

Polio, as I said, isn't an "eliminated disease" yet (as of May 2017), but since you mentioned it, the main places it persists now are Afghanistan and Pakistan.


Shannon diversity index: Pi relates to all found species, or number of species by site? I am trying to dig into Shannon's species diversity index to compare the species diversity between different sites. For this, I need to calculate the 'relative abundance of species within the community'[details here][1]. What I do not understand is if this relative abundance relates to all species in a sample, or all found species?
In my example, I have in site1 6 species: a, b, c, d, e, f and in site2 two species: g, h. Should I calculate the proportion by species by site relative to 6 and 2, or to 8 (6+2, as species do not overlap between the sites? This is dummy example, likely species will reoccur).

If calculated by total number of species (8): Shannon H = 1.11 and 0.820,
if calculated by total number of species by site (6 & 2): Shannon H = 1.29 and 1.26.

I wonder which one is correct? The general trend is the same (site1 is more diverse then site2) but differences between indices seems quite large.
Dummy example to calculate Shannon's H step by step with dplyr. The commented out mutate allows to change if distinct number of species and their sum will by calculated by site or by total.
# Create dataframe with two sites and 6 and 2 different species. Area indicate abundance of species.
d<- data.frame(site = c(rep("s1",6),  rep("s2", 4)),
               species = c(letters[1:6], letters[5:8]),
               area = c(59,12,11,10,5,3,
                        10,5,21,20))

# Calculate sum of the area
# calculate distinct number of species, vary if the distinct area calculates by sum or by total??
d %>%
  mutate(species_n   = n_distinct(species)) %>%   # !! should 'mutate' by placed before the grouping variable or after?
  mutate(species_sum = sum(area)) %>%
  group_by(site) %>%
 #mutate(species_n   = n_distinct(species)) %>%
 #mutate(species_sum = sum(area)) %>%
  mutate(spec_pi     = area/species_sum) %>%
  mutate(pi_ln       = abs(log(spec_pi))) %>%
  mutate(sp_shannon  = spec_pi*pi_ln ) %>%
  mutate(shannon_comun = sum(sp_shannon))

I am trying to dig into Shannon's species diversity index to compare the species diversity between different sites

Shannon's diversity index is a measure of alpha diversity, or diversity within a community. If you are considering each site a different community (which is sounds like you are), then you would calculate Shannon diversity for each site separately, without consideration of the other sites.

What I do not understand is if this relative abundance relates to all species in a sample, or all found species?

Relative abundance is not a function of the number of species found, but the total number of observations collected (similar to sampling effort) at a given site. So, if you made 100 total observations at a site and 10 of those belonged to Species X, the relative (proportional) abundance of Species X is (10 / 100) or 0.1, regardless of the total number of different species present, and regardless of any observations from other sites.
I can't comment on your code, because I don't do tidy-verse. I guess I'm (apparently) old school and still use Vegan and LabDSV for community analysis (I may be biased since I learned community ecology from the author of the LabDSV package). But in general, for any measure of alpha-diversity, each community gets it's own value, and you would not consider any observations from other sites in that calculation, regardless of whether there is species overlap between communities.
For a more direct comparison of diversity between sites, you would use a beta-diversity index like Bray-Curtis dissimilarity, which compares each community to every other community in your analysis.


Where does the energy required to turn ADP into ATP come from? My teacher states that in order to convert ADP into ATP, energy from respiration is required.

However, I watched a video which states that energy from the son is used to turn ADP into ATP.

Which is correct?

This is a common problem when asking about the explanations for things that happen in a biological context.  When you ask for why something happens in biology, the answer to that question depends on what, specifically, you want to know.  For example, the same question, "Why can humans see more colors than dogs?" can be answered using a physiological mechanism (Humans can see more colors than dogs because we have an additional cone type in our eyes), or an evolutionary explanation (Humans can see more colors than dogs because our ancestors were under selective pressure to be able to identify ripe fruit).  Both of these responses would be correct but they are answering from different perspectives.

The question of where the energy comes from to phosphorylate ADP is another one of these questions that can be answered in a couple of different ways.  The immediate mechanism for providing this energy is the proton gradient between the intermembrane space of the mitochondria and the mitochondrial matrix in the case of Cellular Respiration and the proton gradient between the Thylakoid Lumen and the Stroma in the case of Photosynthesis.  But where did the energy ultimately come from?  The sun.  In the case of Photosynthesis, it is energy from the sun that drives the photosystems that generate that proton gradient in the first place.  In the case of your own body, you either eat a plant or eat an animal that ate a plant that got its energy from the sun in the same way, and then use the chemical energy contained in that food to sustain your own proton gradient.  Either way, the energy ultimately came from the sun.  It's just that the proximate (immediate) explanation is a chemical one driven by a chemiosmotic gradient maintained either by sunlight and water in the case of photosynthesis or sugar and oxygen in the case of cellular respiration.