Do electric eels produce current as they just move about, and how/why? https://www.youtube.com/watch?v=y9wktSQdyaE
This video demonstrates how an electric eel can supposedly produce up to 800 watts, and power a Christmas tree, which is very topical (a late Merry Christmas to the Biology community!). The video, sadly, is not very detailed as to how this works.
I was under the impression that electrical discharge was a conscious action on the part of the eel, rather than a natural state for it. But, apparently, the electric eel generates electricity "whenever it moves," as the video's narrator put it? Do electric eels produce electricity subconsciously, just by moving? Surely, though the host lists off the 800 watts of power, it's not constantly producing 800 watts, either?
How do the fish's electrocytes work in this instance, where just lazing about is powering the Christmas tree?

You are right - the 800 Watts are not constantly produced:
There are three types of electrical discharge: (i) low voltage (ii) high voltage doublets or triplets and (iii) high voltage high frequency.
(i) low voltage allows the animal to orient itself in its environment [b].
(ii) high voltage doublets or triplets are used for hunting: By discharging a high voltage doublet or triplet the electric eel induces involuntary twitching in the prey animal. Since this twitching is producing a weak electric field, this allows the electric eel to locate its prey. See Figure 3 of [b].
(iii) high voltage high frequency is used to incapacitate the prey. It's about 400Hz at up to 600V [b]. Wikipedia [c] states that these electric eel can produce about 1Amp of current. That's in the region of 800Watts the narrator is speaking of. Edit2: The pulse duration is about 1ms [e]. With a frequency of 400-500Hz this leads to a surprisingly high ~50% dutycycle. The ability to keep the frequency stable depends on the age (=length) of your eel: The older the eel, the more stable the inter-pulse interval.

Caption: Fig3 from https://doi.org/10.3389/fnint.2019.00023, red=50cm, green=75cm, blue=115cm length of eel
In Figure 5 of [a] you can see that the electrical eel is able capture prey in ~5 sec. During these 5 seconds the electric eel is pretty much constantly producing high voltage discharges. These could be used to light a Christmas tree.
To summarize: Yes - electric eels are very much in control of when and how they discharge. This can be quite clearly seen (or rather heard) in [d] which is  Supplementary Movie 8 from [a]
[a] https://www.nature.com/articles/ncomms9638
[b] https://s3.amazonaws.com/vu-wp0/wp-content/uploads/sites/182/2015/11/Science.pdf
[c] https://en.wikipedia.org/wiki/Electric_eel
[d] https://static-content.springer.com/esm/art%3A10.1038%2Fncomms9638/MediaObjects/41467_2015_BFncomms9638_MOESM559_ESM.mov
[e] https://www.frontiersin.org/articles/10.3389/fnint.2019.00023/full


What is the correct value of Neuronal Resting Potential - is it -65mV or -70mV? Some books show the resting potential of neurons as -65mV, such as Neuroscience: Exploring the Brain, Fourth Edition (2016, published by Wolters Kluwer).

However, a majority of internet sites, including Wikipedia, show the resting potential as -70mV.
Which one of these is the correct value, and why is there this small difference?

Neither is incorrect. Neuronal resting potential is a function of the internal and external concentrations of ions and the conductance of the membrane to those ions via ion channels. Different neurons exhibit a range of resting potentials.

You can calculate the resting potential for a given cell using the Goldman Equation.


What are the total number of action potentials in the human brain? Is there an approximate figure of the total number of action potentials in the human brain? It's my understanding that there are ~ 60 billion neurons in the brain with ~ 100 trillion connections between them. Plus there are graded responses between those connections. Is there an estimated figure for what the total might be?

If firing rate is from 1 Hz to 200 Hz, 100 trillion to 20 quadrillion synaptic firings. Neuronal (say, measured from soma) firings  will add up to 86 billion to 17.2 trillion action potentials per second.

It important to remember, that synaptic firings "sum up" in soma or interfere between each other, so the are more of those.
Read more: http://neuroblog.stanford.edu/?p=4541


Is human mtDNA unique in its single origin? Other than Humans, is there another primate who has a traceable “original Eve mtDNA”?

You can trace back any piece of DNA (from any life form) to a single ancestor called LUCA (Last Universal Common Ancestor), so the short answer is 'yes'. But be careful in your interpretation.

If you look backward in time, you can see that lineages merge (siblings merge first, then cousins merge, etc...) and you necessarily end up with a single individual. In absence of recombination (which is the case for mtDNA), you can always trace back a piece of DNA this way and always find a single ancestor. The age of this common ancestor depends mainly on the population size and demographic history of the lineage. Typically, in a panmictic diploid population of constant size $N$, the expected time to the MRCA (Most Recent Common Ancestor) of the population is $2N$ generations.

So yes, you can find an "original Eve mtDNA" in any species. But please by "original" don't think this ancestor must have represented any novelty or anything of interest and do not make the mistake to think that before this ancestor no one had mtDNA.

The second paragraph is an extremely vulgarized explanation of coalescent theory. You should have a look at an intro to coalescent theory (wikipedia article here) but you might well need an intro to evolutionary biology first. Understanding Evolution might be a good way to go.


What is the difference between a mechanistic and a statistical predictive model? The simplest description of the difference between these two approaches that I have found are on this site who summarise the difference as:

Mechanistic model: a hypothesized relationship between the variables in the data set where the nature of the relationship is specified in terms of the biological processes that are thought to have given rise to the data. The parameters in the mechanistic model all have biological definitions and so they can be measured independently of the data set referenced above.

Phenomenological/Statistical model: a hypothesized relationship between the variables in the data set, where the relationship seeks only to best describe the data.

Could someone exemplify this difference with a short example. I have used and understand the principals of a statistical model (multiple regression etc) but haven't come across any simplistic examples of a mechanistic model and I don't understand what the difference would be in practice.

Edit: I am leaving the question open for a week to see if anyone wants to create a very small 'MWE' of the two types to illustrate what the difference would look like in practice, if not I will accept Memmings answer

Mechanistic model answers the how question. These models are usually biophysically detailed, and designed to be causal. Say you discovered a linear relation between blood pressure drug and heart rate. This would be a statistical model. It doesn't tell you how the two are related biophysically. One could build a detailed model that describes intermediate processes from the drug entering the system, to binding to receptors, and modulating levels of hormones, and acting as a signal to the heart rate modulation system. This model would have more parameters, and if it predicts the phenomena and generalizes well, then it might be a good approximation of the system. Moreover, it generates hypotheses and is more interpretable.

That being said, I do not think the two concepts are mutually exclusive. Some mechanistic/biophysical models can also be statistical at the same time. It's a matter of having enough data and constraints to be able to fit the model or not.


Quantum mechanics in biology There is a growing interest in the applications of non-equilibrium quantum dynamics to describe biological processes (I'm not talking here about Penrose's old theories, but new stuff -- quantum coherence in light harvesting, magnetoreception etc.). What is the biologists' take on this? Is this just a whim of physicists looking for grants, or a serious part of biological research?

Absolutely a serious part of research - quantum mechanics defines chemical structure and reactivity. Whenever you see a headline like 'Scientists find quantum effects important in protein activity, weird huh?', read it as 'Scientists find pragmatic classical approximations inadequate in describing protein activity'.

In protein structure, for example, classical molecular dynamics/mechanics are important in generating computationally tractable problems, however they represent a tacit and streamlined parameterisation of underlying quantum mechanics. QM protein structures are usually too gnarly to compute (at least historically speaking), except in regions of interest like an active site, where a model fine-tuned for sequences of amino acids will probably fail badly anyway. As a concrete example, the group that I'm in is in part interested in computationally modelling the active site of plant photosystem II, which contains a cluster of spin-coupled manganese atoms. To glean any useful understanding of how this cluster functions via a computational model, an explicit quantum mechanical level of theory that takes into account electron exchange and correlation must be used. This requirement can probably be extended to any metalloenzyme.

And this isn't touching upon the resonance hole transfer that oxidises the active site, the Davydov solitons that manifest in protein alpha helices, or indeed the quantum electrodynamical origins of the Van der Waals interaction that causes everything to tend to stick to everything else.

Hope this is interesting :D

(note: I am not involved with PetaChem, I just think it's freaking awesome.)


Lysozyme amino acid sequence: N-terminal extension I looked up the amino acid sequence of lysozyme here: http://www.biology-pages.info/L/Lysozyme.html

Then I crossed referenced that with the lysozyme sequence on UniProt: https://www.uniprot.org/uniprot/B8YK79

My question is why does the sequence on UniProt start with eighteen other amino acids before getting to the start of the sequence described in the first source?

The sequence on UniProt starts with "MRSLLILVLCFLPLAALG".  I know the M comes from the start codon in the gene for the protein, but where does the rest of this come from?

If you scroll down through the uniprot entry you will come to a section with the heading PTM/Processing.

From this you can see that the first 18 amino acids are a signal peptide.

You can learn more about signal peptides from any good introductory textbook covering cell-biology — alternatively Khan Academy is a good source for learning the basics.


Is there a specific suffix for "within a cell"? i.e. in a similar manner to how -aemia refers to within the blood Words like hyperglycemia and hyponatremia refer to the relative level of each component in the blood, not in the cell. Is there a suffix for within the cell? For reference I would like one word as an alternative to "hyperglycemic cell".

"Cyto"/"cytic" and similar are common prefixes/suffixes to refer to things associated with cells; however they don't necessarily specify intracellular space, they are more often referring to specific cell populations, counts, etc.

The word "intracellular" is, however, commonly used terminology for "inside the cell."

For the specific case you mention, I would simply write "high/elevated intracellular glucose" - I am unaware of any reference that uses a individual word for the same meaning. Some others have referred to "intracellular hyperglycemia" which may be a bit odd since the -emia refers to the blood, but they are specifically referring to the case where high intracellular glucose is a direct consequence of overall hyperglycemia.


Why are compost worms sensitive to light? I read that compost worms dislike light. But I'd say they don't have eyes and I couldn't imagine their skin is sensitive to light in general, is it? And if so, then why?

It will sounds counter-intuitive you but earthworms do sense light with their skin. They don't have eyes but they have specialized nerve ending equipped with photoreceptor cells. They are all over skin but concentrated towards first segment of worm. Prostomiun are main light sensing organ in worms. Following image shows their position in first segment of earthworm. (Image source: cronodon.com).

Closer look of above image taken from same website,

Structure of photoreceptors

Earthworm have microvillar photoreceptors like insects (Rohlich et al 1970). Detailed structure is discovered long back.

There is not much information about phototrasnduction in worms but it is well characterized in it's close relative C. elegans (Ward et al 2007).

Now coming to why part, you might wonder if they are spending most of time buried why do they need photoreceptors ? @AMR has guessed it correctly. They use this as protective system. Photoreceptors helps them providing information about how near they are to surface because UV radiation will harm them or probably kill. If there is higher light sensing, they go back to darker regions. You can find similar information from UMICH press release.


Is there evidence to suggest that sleeping requires more energy than watching TV? I have heard the claim:

  sleeping requires more energy than watching TV.

I have heard the counter-claim - watching TV requires large amounts of energy.

My question is: Is there evidence to suggest that sleeping requires more energy than watching TV?

From Harvard Health Publishing. The weights are in pounds, and the energy is shown in calories. These values are for over a 30 minute period.

This suggests that the claim is false; watching TV uses more energy than sleeping does.


DNA content doubling in interphase Why does the DNA content of a cell get doubled in interphase? Why doesn't it become tripled or quadrupled? What's stopping it from doing so?

So in mitosis, the cell has to split itself into two cells; each daughter cell has a functional genome that may again split into more daughter cells. The cell replicates the DNA before dividing, so the error in replicating 3x or 4x is that upon division, the daughter cells will have more DNA than the initial cell, and every generation will have more DNA than the last. One replication ensures both daughter cells receive one functional genome. We can see the result of extra DNA in cases like Down Syndrome (trisomy of chromosome 21).
The cell controls this process by controlling the cyclins present in the cell temporally, namely cyclin-A and cyclin-E when we talk about DNA replication in S-phase,

From wikipedia,

Cyclin A resides in the nucleus during S phase where it is involved in the initiation and completion of DNA replication. As the cell passes from G1 into S phase, cyclin A associates with CDK2, replacing cyclin E. Cyclin E is responsible for initiating the assembly of the pre-replication complex. This complex makes chromatin capable of replication. When the amount of cyclin A/CDK2 complex reaches a threshold level, it terminates the assembly of the pre-replication complex made by cyclin E/CDK2. As the amount of Cyclin A/CDK2 complex increases, the complex initiates DNA replication.
Cyclin A has a second function in S phase, in addition to initiating DNA synthesis, Cyclin A ensures that DNA is replicated once per cell cycle by preventing the assembly of additional replication complexes. This is thought to occur through the phosphorylation of particular DNA replication machinery components, such as CDC6, by the cyclin A/CDK2 complex. Since the action of cyclin A/CDK2 inhibits that of cyclin E/CDK2, the sequential activation of cyclin E followed by the activation of cyclin A is important and tightly regulated in S phase.

Source: Cyclin A


What keeps the resting potential of neurons constant at -70 mV? I know the sodium-potassium pump pumps out 3 Na+ ions and pumps in 2 K+ ions per reaction so the negative charge in the axon increases. However, once the voltage (difference of charge inside and outside of the neuron) gets down to -70 mV, this stops going further below. Why?

I know that this is because of other transport proteins and the presence of anions and cations in the axon, but what are those proteins and ions precisely? There are always negatively charged proteins inside a cell, including a neuron, so I assume there must be a strong force which keeps the voltage from going down.

By the way, is the opening and closing of an ion channel triggered by the voltage of the neuron or the concentration of the ion?

The neuronal cell membrane is quite permeable to K+. Because the Na+,K+-ATPase pumps K+ inside of the cell, K+ tends to diffuse outward again, thereby taking positive charge outside the cell and making it negative inside (see Further Reading 1). This outward flow of K+ stops at a certain point, because the driving force of K+ diffusion out of the cell along with its concentration gradient, equals the charge gradient, which becomes more and more negative inside the cell as more K+ diffuses out (see Further Reading 2). Hence an equilibrium is reached which is close to the resting membrane potential of -70 mV. Other ions such as Cl- are also relatively permeable and affect the resting membrane potential (see Further Reading 1). Ions such as Na+ and Ca2+ are typically highly impermeable and do not substantially affect the resting potential.

As to your second sub-question:voltage-gated channels are gated through voltage differences (Purves et al., 2001), not ion concentration differences.

Further Readings
1. If the average resting potential of a neuron is -70 mV, why is there such a high ratio of K+ ions inside relative to out?
2. Why do negative ions flow into a cell in an inhibitory synapse, even though a neuron has a negative resting potential?

Reference
-  Purves et al., Neuroscience (2001). 2nd ed. Sunderland (MA): Sinauer Associates


Do all RNA polymerase in Eukaryotes share the same transcription factors? I know that TFII proteins bind to cis elements in DNA and help initiate transcription for RNA polymerase II. But do RNA polymerase I and III also use these proteins when transcribing genes? Also, do all genes require promoters/cis elements? Do all genes put in a vector require promoter regions/cis elements?

Except for the TATA-binding protein (TBP), there are no common transcription factors for each RNA polymerase. However, there are homologies between many of the factors used by the different enzymes.

The paper Conservation between the RNA Polymerase I, II, and III Transcription Initiation Machineriesa gives a good overview over the different initiation factors of each RNA polymerase enzyme. It contains a comparison of various transcription factors in yeast.

Here is an excerpt form the paper showing the homologies between some of the initiation factors of the TFII group and their homologous counterparts. (The first schematic is RNA poly II, the second RNA poly I, and the third RNA poly III):

Source:

a Alessandro Vannini, Patrick Cramer, Conservation between the RNA Polymerase I, II, and III Transcription Initiation Machineries, Molecular Cell, Volume 45, Issue 4, 24 February 2012, Pages 439-446, ISSN 1097-2765, https://doi.org/10.1016/j.molcel.2012.01.023.


How does aging affect fingerprint? Do fingerprints change as we grow from child to adult? Most notably, what is the effect of the increase in surface area of palms and fingers on the finger print? Does the finger print simply increases in size, and/or does the pattern change?

And what about old age? As the connective tissue in dermis get lax, how is the fingerprint affected?

Fingerprints form in the womb at 22 weeks and after that, all they will do is expand as you grow. Therefore, it is possible that a fingerprint 22 weeks after conception could be used to identify a 50-year-old criminal.


How many genes do we share with our mother? Somewhere I have read we share more than 99% of our genes with every other other person and 98% of our genes with chimpanzees. What does this mean? Don't we share 50% of our genes with our mother and 50% with our father?

I've found an another article stating that.

There is a distinct difference between the 'genes' that we share, and the genome (the DNA) that the genes are made of.

All humans (excluding genetic disorders) have the same genes, but the same gene in different individuals may have a slightly different DNA sequence, and this may be manifested in the different traits you can observe between people (eye colour, height, etc) or be ’silent’ (have no observable effect).

So you therefore have 100% of the genes that your mother has.

However, as stated in another answer, you inherit the different 'alleles', or versions, of the genes from your parents, and end up with ~50% of the alleles from each parents (but all the genes).

With regard to species differences; many of the genes we inherit have evolved over millions (in fact billions) of years, and thus many of our genes are present in most other organisms (but in very different forms - the DNA). Chimpanzees are our closest relatives in evolutionary terms, and thus their genes are very similar to ours in the genome (~98% the same). But this only applies to the coding regions! Less than 2% of your genome actually codes for genes - the rest is mostly regulatory (not junk, as it used to be called), and this is where the true inter-species variation lies. So whilst we have ~98% homology in the protein-coding regions, this is MUCH less if you count the whole genome.


What are these bugs skittering about the kitchen sink? I found a bunch of these around a kitchen sink in an apartment building in Toronto, Canada, in late October, 2019.

The bugs vary in size, but are all very tiny, less than one millimeter (the photos were taken with a macro lens, and still barely captured them).

They move very fast when they detect light changes, and hide in the crevices around the sink.

They die very easily when squashed.

Edit: Managed to shoot a larger, more photogenic specimen.

Those are springtails, order Collembola. Looks like they are in the family Entomobryidae. They are completely harmless. They don't bite, or spread disease. They often find their way into potted plants in people's homes. I'm not surprised that they are in your sink. Their small size makes them subject to desiccation.
https://en.wikipedia.org/wiki/Springtail https://en.wikipedia.org/wiki/Entomobryidae


Genomic location-coordinate of RdRp of SARS-CoV2 I understand that nsp12 is the RdRp protein in the ORF1 of SARS-CoV2 genome. And nsp12 starts from the starting nucleotide base of orf1ab. Could you please tell me the exact genomic location coordinate of RdRp?

Is there and database from where the FASTA sequence (nucleotide and aa) of RdRp of SARS-CoV2 can be obtained?

Any answer to this question would be highly appreciated.

A useful database and exploratory tool is the UCSC Genome Browser wuhCor1 assembly browser instance.

A synonym for nsp12 is Pol. Its position range in the wuhCor1 assembly is NC_045512v2:13,442-16,236.

There are several ways to extract sequence, but one programmatic way is to get the FASTA from UCSC Goldenpath for the assembly, and extract the characters of interest from the position range for the gene of interest using standard Unix tools:

$ wget -qO- ftp://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/chromosomes/NC_045512v2.fa.gz | gunzip -c | tail -n+2 | tr -d '\n' | cut -c 13442-16236 | awk '{print ">nsp12"; print $0}' > nsp12.fa
$ cat nsp12.fa
>nsp12
TCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTGCAGCCCGTCTTACACCGTGCGGCACAGGCACTAGTACTGATGTCGTATACAGGGCTTTTGACATCTACAATGATAAAGTAGCTGGTTTTGCTAAATTCCTAAAAACTAATTGTTGTCGCTTCCAAGAAAAGGACGAAGATGACAATTTAATTGATTCTTACTTTGTAGTTAAGAGACACACTTTCTCTAACTACCAACATGAAGAAACAATTTATAATTTACTTAAGGATTGTCCAGCTGTTGCTAAACATGACTTCTTTAAGTTTAGAATAGACGGTGACATGGTACCACATATATCACGTCAACGTCTTACTAAATACACAATGGCAGACCTCGTCTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGACACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATGATTTTGTAGAAAACCCAGATATATTACGCGTATACGCCAACTTAGGTGAACGTGTACGCCAAGCTTTGTTAAAAACAGTACAATTCTGTGATGCCATGCGAAATGCTGGTATTGTTGGTGTACTGACATTAGATAATCAAGATCTCAATGGTAACTGGTATGATTTCGGTGATTTCATACAAACCACGCCAGGTAGTGGAGTTCCTGTTGTAGATTCTTATTATTCATTGTTAATGCCTATATTAACCTTGACCAGGGCTTTAACTGCAGAGTCACATGTTGACACTGACTTAACAAAGCCTTACATTAAGTGGGATTTGTTAAAATATGACTTCACGGAAGAGAGGTTAAAACTCTTTGACCGTTATTTTAAATATTGGGATCAGACATACCACCCAAATTGTGTTAACTGTTTGGATGACAGATGCATTCTGCATTGTGCAAACTTTAATGTTTTATTCTCTACAGTGTTCCCACCTACAAGTTTTGGACCACTAGTGAGAAAAATATTTGTTGATGGTGTTCCATTTGTAGTTTCAACTGGATACCACTTCAGAGAGCTAGGTGTTGTACATAATCAGGATGTAAACTTACATAGCTCTAGACTTAGTTTTAAGGAATTACTTGTGTATGCTGCTGACCCTGCTATGCACGCTGCTTCTGGTAATCTATTACTAGATAAACGCACTACGTGCTTTTCAGTAGCTGCACTTACTAACAATGTTGCTTTTCAAACTGTCAAACCCGGTAATTTTAACAAAGACTTCTATGACTTTGCTGTGTCTAAGGGTTTCTTTAAGGAAGGAAGTTCTGTTGAATTAAAACACTTCTTCTTTGCTCAGGATGGTAATGCTGCTATCAGCGATTATGACTACTATCGTTATAATCTACCAACAATGTGTGATATCAGACAACTACTATTTGTAGTTGAAGTTGTTGATAAGTACTTTGATTGTTACGATGGTGGCTGTATTAATGCTAACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGACTTTATTATGATTCAATGAGTTATGAGGATCAAGATGCACTTTTCGCATATACAAAACGTAATGTCATCCCTACTATAACTCAAATGAATCTTAAGTATGCCATTAGTGCAAAGAATAGAGCTCGCACCGTAGCTGGTGTCTCTATCTGTAGTACTATGACCAATAGACAGTTTCATCAAAAATTATTGAAATCAATAGCCGCCACTAGAGGAGCTACTGTAGTAATTGGAACAAGCAAATTCTATGGTGGTTGGCACAACATGTTAAAAACTGTTTATAGTGATGTAGAAAACCCTCACCTTATGGGTTGGGATTATCCTAAATGTGATAGAGCCATGCCTAACATGCTTAGAATTATGGCCTCACTTGTTCTTGCTCGCAAACATACAACGTGTTGTAGCTTGTCACACCGTTTCTATAGATTAGCTAATGAGTGTGCTCAAGTATTGAGTGAAATGGTCATGTGTGGCGGTTCACTATATGTTAAACCAGGTGGAACCTCATCAGGAGATGCCACAACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTCACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTACAACACAGACTTTATGAGTGTCTCTATAGAAATAGAGATGTTGACACAGACTTTGTGAATGAGTTTTACGCATATTTGCGTAAACATTTCTCAATGATGATACTCTCTGACGATGCTGTTGTGTGTTTCAATAGCACTTATGCATCTCAAGGTCTAGTGGCTAGCATAAAGAACTTTAAGTCAGTTCTTTATTATCAAAACAATGTTTTTATGTCTGAAGCAAAATGTTGGACTGAGACTGACCTTACTAAAGGACCTCATGAATTTTGCTCTCAACATACAATGCTAGTTAAACAGGGTGATGATTATGTGTACCTTCCTTACCCAGATCCATCAAGAATCCTAGGGGCCGGCTGTTTTGTAGATGATATCGTAAAAACAGATGGTACACTTATGATTGAACGGTTCGTGTCTTTAGCTATAGATGCTTACCCACTTACTAAACATCCTAATCAGGAGTATGCTGATGTCTTTCATTTGTACTTACAATACATAAGAAAGCTACATGATGAGTTAACAGGACACATGTTAGACATGTATTCTGTTATGCTTACTAATGATAACACTTCAAGGTATTGGGAACCTGAGTTTTATGAGGCTATGTACACACCGCATACAGTCTTACAG

Another option is to visit the Pol link again and look for the "View DNA for this feature (wuhCor1/SARS-CoV-2)" link, click on it, and click on "get DNA" to get a similar FASTA file. But if you're going to do bioinformatics, knowing how to string together Unix tools is a valuable skill.

To get the amino acid sequence, visit the Pol link, look for the Swiss-Prot record information, and do a search through UniProt for the record P0DTD1.

Via the "RNA-directed RNA polymerase" entry for P0DTD1, you can click on the "RNA-directed RNA polymerase" post-translation product to get to a record with the amino acid sequence: https://www.uniprot.org/blast/?about=P0DTD1[4393-5324]&key=Chain&id=PRO_0000449629


How sterile is working next to a bunsen burner? When I was still doing lab work, many people would just wear gloves and work next to a bunsen burner because the clean benches were all in use.

This was mostly for plating bacteria like Bacillus subtilis. The equipment had been autoclaved, of course, but is just having the bunsen burner next to you without working in a clean bench really enough to avoid contaminating your plates?

For doing bacterial work on an open bench, this is standard "Sterile Technique." The updraft from the heat generated by the Bunsen Burner should create a relatively sterile field with which to work, so long as you aren't breathing directly on your plates.

Also part of sterile technique is to "flame" all of your pipets, agar plates, and the openings of bottles to remove any contaminants from those areas, and also to protect them from getting into sterile mediums. Every time you uncap or cap a media bottle or test tube you are suppose to quickly pass it over the flame. Obviously these days, plastic equipment makes that a little less practical, but it still can be done if you pass quickly and aren't too close to the flame.

Disposable serological pipettes should remain covered until just before use and then the "banana peel" method of removing the wrapper should be used. If the tip touches anything it should be discarded.

The true test of your sterile technique is whether or not you are getting contamination. Some labs that work with recombinant bacteria don't even bother with sterile technique for bacteria work as they are using antibiotic selection, and contamination becomes much less of a concern. That being said, an ounce of prevention is worth a pound of cure, so if you keep your work space clean, and there isn't a risk of fire, i.e. you don't have organic solvents in the area or the stack of lab reports you are supposed to grade spilling over onto your bench, then it doesn't hurt to light up a burner even if you are using selection.

You are also supposed to have cleaned your work space prior to lighting the burner with 70% ethanol, which will rather quickly kill most bacteria on the surface. Wearing gloves and proper glove technique also helps keep contamination to a minimum. Keeping hair tied back and wearing a clean lab coat can also help, though lab coats are usually more for your protection and for the protection of others (not transmitting hazardous materials on your personal clothing) than to prevent contamination.

Most people get the false impression about BSL-2 Laminar flow cabinets or glove boxes are suppose to be sterile and prevent contamination. Their real purpose is to keep things in, not really to keep things out. Laminar flow hoods will keep aerosolized particles within them from getting to you, so long as you keep the hood area fairly clear and do not block vents, but as you pass your hands through the flow, you are bring whatever is on you and has tagged along for the ride into to work field. Glove boxes can maintain a sterile field, so long as it, and everything going into it, other than your samples have been sterilized, and your sample hasn't already been contaminated.


I found these in my bathroom and WC Are they somehow dangerous? What are they and how can I get rid of them?

These are silver fish (Lepisma saccharina) and harmless. Wikipedia says (image taken from the article):

  Silverfish are nocturnal insects typically 13–25 mm (0.5–1.0 in)
  long. Their abdomens taper at the end, giving them a fish-like
  appearance. The newly hatched are whitish, but develop a greyish
  hue and metallic shine as they get older. They have two long cerci
  and one terminal filament at the tips of their abdomens; the filament
  projects directly off of the end of their body, between the left and
  right cerci. They also have two small compound eyes, despite other
  members of Zygentoma being completely eyeless, such as the family
  Nicoletiidae.

  Like other species in Apterygota, silverfish are completely
  wingless. They have long antennae, and move in a wiggling motion
  that resembles the movement of a fish. This, coupled with their
  appearance and silvery scales, inspires their common name. Silverfish
  typically live for two to eight years. Silverfish are agile runners
  and can outrun most of their predators (including wandering spiders
  and centipedes). However, such running is possible only on horizontal
  surfaces, as they lack any additional appendages, and therefore are
  not fast enough to climb walls at the same speed.[citation needed]
  They also avoid light.


what is linkage disequilibrium supposed to measure? During reading about genetics I came across with the term of linkage disequilibrium, and I do not really understand what it supposed to mean. What is linkage disequilibrium? My current understanding that it is "deviation from independent assortment",

Linkage disequilibrium refers to a situation whereby two or more alleles, from different loci, segregate non-randomly. Therefore we have a statistical association between this two alleles.
The linkage disequilibrium can be used in gene mapping, because we assume that these loci are in the same region on the chromosome. The more often they appear together, the more they segregate non-randomly, the closer they should be on the chromosome.

http://www.researchgate.net/post/What_is_the_difference_between_Linkage_Equilibrium_and_Linkage_Disequilibrium


Are bleach solutions still routinely used in biochemistry laboratories to rid surfaces of bacteria, viruses, certain enzymes, and nucleic acids? Decades ago I would stop by biology and biochemistry laboratories to see what was up, and I noticed a ubiquitous presence of a squirt bottle of bleach solution. When I asked what it was for I would get different answers in different laboratories. They ranged from disinfection of surfaces by accidental bacteria or phage contamination to denaturing of certain specific proteins or nucleic acids thought to be threatening to certain types of experiments.
Experimental techniques have developed dramatically over the subsequent decades.
Question: Are bleach solutions still routinely used in biology and biochemistry laboratories to rid experimental surfaces of bacteria, viruses, certain enzymes, and nucleic acids? If so, how can one solution be so reliably useful across all of these cases?

I'm a research post-doc working in a US-based microbiology research lab. We still use a relatively low-concentration bleach solution to decontaminate most liquid cultures before disposing of them, but most of our surface and equipment decontamination is accomplished with alcohol (either ethanol or isopropyl alcohol (IPA)). We do work with some organisms that are not effectively killed by alcohol, such as C. difficile. C. difficile makes endospores which are very resistant to alcohol-based agents, but they are readily killed by bleach.
So after working with C. diff and other spore-forming bacteria we decontaminate with commercial wipes containing a stabilized sodium hypochlorite solution at a little less than 1%, which isn't even enough to give off a strong bleach odor. On metallic surfaces and some kinds of rubber, we follow up with an alcohol wipe to prevent corrosion from the bleach.
We do have other sporicidal agents that are used for specific applications where bleach isn't suitable, but most of them are much more harsh (requiring use of respirators), require a longer contact time, and have a substantially shorter shelf life at the effective concentration (sometimes just days or hours, vs. months with bleach).
Bleach is also good for destroying DNA and RNA in clean areas used for PCR setup, but there are some commercial products specifically designed to do this along inactivating nucleases that might degrade a sample, so I personally use those products. (Note that ethanol and IPA solutions can actually precipitate nucleic acids, leaving them behind after the solution evaporates.)


Human disease and associated phenotype database? Does anyone know of any good databases that contain symptoms for diseases and other ailments in humans? I've tried working with UMLS, but thats been impossible to work with. I've also tried working with the disease ontology website (http://www.disease-ontology.org/), but that doesn't seem to be very...comprehensive...in terms of symptoms for the diseases they have.

I've tried looking at the the disease database (http://www.diseasesdatabase.com/), but they are reluctant to hand over the raw data, if I understand correctly.

Anyone have better ideas?

It seems to me like you're effectively wanting to make a decision matrix.

So... As said above, ICD and SNOMED CT going to have codes for your diseases and symptoms. I'd lean toward SNOMED CT due to the way it organises concepts. Essentially from broad to specific. That way users can enter very specific symptoms, and your matrix only needs to have symptoms as specific as is required.
For example you can say "vomitting" is a symptom of "alcohol poisoning" in your db. And if a user enters "projectile vomitting" the SNOMED structure recognises this as a type of vomitting.

However - Symptoms don't make the disease, and most diseases have a huge array of 'possible symptoms' (Which is why SNOMED CT doesn't have such relationships). So it's not an easy undertaking. Hence why those who've made such db's (as you've linked to) are reluctant to share their IP, at least without $$$.

If you're going to make your own, here's some tips.
Consider:

only diseases relevant to your use case - eg. Aged care doesn't require paediatric disorders;
exclude non-specific symptoms;
rank your symptoms by frequency - eg. 60% of pregnant women have morning sickness, where as 100% have an HCG > 10*

Hope this helps. And good luck.

edit- there is a similar thread on LinkedIn

*fabricated statistic :).


How many species have existed on earth? I found a paper estimating the number of species currently living on earth. Now I'm wondering If anybody tried to estimate the number of species that have lived on earth. I'm familiar with problems of "species concepts". But I'm sure, there is at least a number of all known fossils.

EDIT: In contrast to the question How many organisms have ever lived on Earth?
I'm asking for species and not for individuals. The answer to my question can be used to ansewer the queston for the number of organisms. But still, The questions is different.

A quote from a Discovery movie:

  Scientists have estimated that over the course of Earth's history, anywhere between 1 and 4 billion species have existed on this planet.

I know, I know... sorry. I hope someone has the original research, but in case no one does, or if you are just curious, and Discovery is fine for you, I decided to share what I know for the time being.


What is the effective relatedness of inbreeding? If a human inbreeds with a relative, how distant does the relative have to be before the homozygosity in the child is no higher than if the mate were randomly chosen from the global population?

In "The Selfish Gene" Dawkins claims a relatedness factor of 1/128 to be pretty much the same as the baseline chance for the rest of the population to have the same gene, so that would be a third cousin. (Or your great great great great great grandparents, though an incestuous relationship with them is quite unlikely I think.)

I'm not sure where he got that from though.


Why don't Australian magpies in Tasmania swoop at people? I'm currently living in Tasmania (Australia) and I have noticed that Magpies don't swoop at you here, yet they do in other parts of the country.

Just wondering: does anyone know why?

I cannot give you a proved explanation of why magpies don't swoop in Tasmania. Nevertheless, my goal here is corroborating your impression with some data, and indicating a possible cause.

Aussie Magpies and swooping

Australian magpies are not the same species of European magpies (Pica pica). Actually, they are not even corvids. They belong to the Family Artamidae, and their scientific name is Gymnorhina tibicen (synonym: Cracticus tibicen). Here is a male magpie (you can tell he's a male by the white colour in his back):

Australian magpie in Victoria

Magpies are territorial birds and in the breeding season (which is right now, as I write this, in September) a small percentage of the males become quite aggressive towards people approaching the nest.

According to the Wikipedia link above:

  These magpies may engage in an escalating series of behaviours to drive off intruders. Least threatening are alarm calls and distant swoops, where birds fly within several metres from behind and perch nearby. Next in intensity are close swoops, where a magpie will swoop in from behind or the side and audibly "snap" their beaks or even peck or bite at the face, neck, ears or eyes. More rarely, a bird may dive-bomb and strike the intruder's (usually a cyclist's) head with its chest.

Cyclists are well known targets:

As a personal and anecdotal note, I have to say that I bike during the breeding season and I was never attacked by a magpie, nor I've ever seen a magpie swooping.

No swooping in Tasmania

Your claim sounded quite incorrect to me when I first read your question. After all, the magpies in Tassie (short for Tasmania) and the magpies in the mainland belong to the same species (G. tibicen).

However, after some research, your claim seems to be correct: there is very few, if any, report of magpies swooping in Tassie.

For instance, this is a chart from the Magpie Alert website:

As you can see, there is no registered attacks in Tassie (TAS) from 2013 to 2017.

And here is a map of the attacks (the online version is here):

Most of the attacks happen in Victoria and New South Wales. However, besides Tasmania, you can see both in the chart and in the map that there is no attack registered in Northern Territory (NT) and New Zealand (NZ) as well.

That data doesn't prove that there is no swooping in Tasmania, but it does show that, somehow, Tasmanian magpies behave differently. Maybe they are more shy, or maybe the males over there perform other behaviours to drive off intruders before swooping. It's also possible that the explanation is completely different: maybe people in Tasmania don't like to go online and complain about magpies.

A possible cause

The Tasmanian magpie (G. tibicen hypoleuca) is the smallest magpies of all in Australia. Besides that, it is the magpie that forms the largest groups (Kaplan, 2004), with as many as 15 individuals.

Tasmanian magpie, also a male

Coincidentally, magpies form smallest groups exactly in the areas of higher incidence of swooping, like Victoria and New South Wales. The possible correlation among those variables (swooping rate, body size and group size) is something that is still to be investigated.

Conclusion

However, regardless the actual explanation, the fact is that the number of registered attacks in Tassie is, indeed, smaller than in the mainland. After doing a lot of research, the explanation for this remains unknown to me. Let's wait for more answers.

PS: as I said in my comment, magpies are not that aggressive: they are very nice birds and very intelligent ones as well. So, one way to avoid attacks from the magpies in your area is becoming friends with them: magpies have a good memory and they can recognise a face after years. So, if you become friends with your local magpies, they probably won't attack you if you get closer to the nest. By the way, the best way to making new friends is with food (that works with humans too).

Source: Kaplan, G. (2004). Australian Magpie: Biology and Behaviour of an Unusual Songbird (Australian natural history series). CSIRO Publishing.


Exercise vs stimulants, which is more effective for promoting concentration? Stimulants are the first choice for treating ADHD. But we also know that exercise helps to improve concentration.

We know that both stimulants and exercise increase bloodflow to muscles and to the brain by activating the sympathetic nervous system. Is this is the MAIN cause of the effect of improved concentration, rather than, say, specific activation of parts of the brain responsible for learning or planning or something similar?

What I'm asking is, do drugs and exercise have different effects on the brain, what are the differences, and what are the consequences of these differences on concentration and learning? Which is more effective for promoting concentration and why?

exercise stimulates brain regions that are involved in memory function to release a chemical called brain-derived neurotrophic factor (BDNF) which is a protein that helps in the survival of neurons and promotes the growth of new neurons. BDNF rewires memory circuits so they work better.

Memory enhancers or smart drugs or Nootropics as they are called help in improving the efficiency of neurotransmitters and its associated receptors in cognitive function. Three systems that are stimulated by these drugs which I could find are:

1) Cholineric System

2) Glutamatergic System

3) Dopaminergic & Serotonergic Systems

You can read about about them here along with links to published articles on their effects. Details of different nootropic drugs are mentioned in this article along with their effects.

Of course naturally improving concentration would be the way to go considering the hazards of long term use of drugs. Some links to the side effects are this and this


What would it take to recognize a deer by its photo? I am trying to recognize a deer by its antlers or any other means.
Elaborating:
I was hoping to use their antlers to recognize them but I have heard that most deers shed their antlers every year so it would be difficult to recognize it from the last year's photo unless these antlers retain the same pattern every year.

If not the antlers, what other characteristics should I be looking for?

Is there any software that can help me in recognizing a deer?

There is a lot of variation in how and when deer shed their antlers. In most arctic and temperate-zone species, antler growth and shedding is annual, and is controlled by the length of daylight. In tropical species, antlers may be shed at any time of year, and in some species such as the sambar, antlers last several years. Some equatorial deer never shed their antlers.

The horns change every year and, especially, increase the number of branches (and consequently, change their shape). You can't recognize them by antlers, but by other features, such as color of the hair or the lineaments. Like us, animals have individual morphological differences that are recognizable and listable.

Biologists specializing in studies of particular animal species not only take photos, but also make drawings and write descriptions of behavior, to identify individuals within herds.

An optical examination, however, of the subject through drawings and photos (and if possible, direct observation), is more useful than a PC program. This involves identifying particular similarities and equalities that are not "identical". This is possible to do visually on a large (but limited) number of specimens. The human eye is the best computer.


Why don't all plants grow like weeds? I'm well aware of the Gardening/Horticultural approach of "a weed is any plant that you don't want in its current location".
But I think most people would agree that there's a more useful interpretation of "weed" that relates to its growth.
I would say that weeds are the plants that would be extremely easy to introduce if you wanted to them in a particular place, and extremely hard to remove if you didn't want them.
Common properties that I can think of, of the top of my head, for such plants include:

quickly growing.
quickly reproducing.
self-seeding.
re-growing from roots even if the above-ground plant is removed.
not particularly sensitive to ground conditions.

Question:
Why don't all plants exhibit these behaviours?
It feels relatively "obvious" that the plants that exhibit these behaviours should be able to out-compete plants that don't, since they reproduce faster and are more resilient.
And yet the slightest glance outside demonstrates a wide variety of plants that I think would trivial die if I attempted to attack / damage them.
What gives?

every advantage has a disadvantage.
self seeding means less genetic diversity, fast growing also means more energy requirements  and even a structurally weaker plant, fast reproducing means tiny sieeds so individual seeds have a very small chance of survival. Biology is all about cost vs benefit, there is no such thing as universal advantage.
regrowing is actually something all plants can do provided they have enough resources, this is one way humans replicate crops. Weeds are often more sensitive to ground conditions, and don't do well in places where humans have not cleared and irrigated the land. weeds are often pioneer species good at taking over open land, one effective way to deal with weeds is to plant a cover crop because weeds can't actually compete well when there is already healthy grass. Many crops on the otherhand are being grown in sub-optimal conditions, in climate/soil other than the the one they evolved for while weeds tend to be native plants already adapted for the local conditions.


How does Halosulfuron-methyl kill nutsedge, while leaving lawn grass and most weeds undamaged? I use Halosulfuron-methyl to control yellow and purple nutsedge in lawns. This chemical acts by interfering with the acetolactate synthase enzyme, which quickly slows cell division, and growth at all points.

How does this work without also interfering with enzymes in the lawn grass?

Halosulfuron-methyl is a member of the family of sulfonylurea herbicides. Brown (2006) mentions in his abstract the following, and I quote:

  This class of herbicides acts through inhibition of acetolactate synthase [...], thereby blocking the biosynthesis of the branched-chain amino acids valine, leucine and isoleucine. This inhibition leads to the rapid cessation of plant cell division and growth. [...] Crop selectivity results from rapid metabolic inactivation of the herbicide in the tolerant crop. Under growth-room conditions, metabolic half-lives in tolerant crop plants range from 1–5 h, while sensitive plant species metabolize these herbicides much more slowly, with half-lives > 20 h. Pathways by which sulfonylurea herbicides are inactivated among these plants include aryl and aliphatic hydroxylation followed by glucose conjugation, sulfonylurea bridge hydrolysis and sulfonamide bond cleavage, oxidative O-demethylation and direct conjugation with (homo)glutathione.

Hence, metabolic inactivation activity differs between susceptible and insusceptible species. To get to your question: this means that the enzymes in lawn grass are also inhibited, but to a lesser extent, as the herbicide is metabolized and inactivated more rapidly in grasses.

Reference
Brown, Pesticide Science 2006;29:241–378


Chemosynthesis in Bacteria The light reactions, if seen as a whole, are basically the oxidation of water to provide energy (ATP) to fuel the Calvin Cycle. The photons provide the activation energy for the same.

How then can we say that during chemo-synthesis bacteria get ATP in the first step by oxidizing inorganic substances like $H_2S$ or $CH_4$ because ultimately, it is similar to the light reactions and will require some activation energy?

Where does this energy come from?

These chemo-synthetic bacteria gets energy from oxidation of inorganic compounds. Following table from Biology of Prokaryotes shows main reactions used by different species,

This oxidation happens only if electron acceptor is available. These all reactions have negative Gibbs Free Energy, hence they are favorable reactions and happens spontaneously. Generally oxygen is preferred electron acceptor but in case of lack of oxygen nitrate, sulfate, $HCO^{3-}$ etc are used.


Can anyone (urgently) tell me if this is a bed bug We just arrived in a place where a lot of people were living before.

This is what we found on the mattress and we are curious to see if this is a bedbug, or some harmless species; To know if we go out right away or not :)

Location: Poland. ;  Size: ~13mm long

Here is a photo with a measuring tape next to it:

Closeup:

This is not a bedbug. This is a hemipteran called a leaf-footed bug in the Coreidae family. (Note: bedbugs are also in the order Hemiptera, but in a different family).
Species similar to yours found in Poland include Coreus marginatus (or "dock bug"), which [according to Wikipedia], is found throughout Europe.

 Adult male and nymph shown from dorsal and ventral views. Source: Wikipedia
C. marginatus is typically 13-15 mm long (which matches your updated length) and has a widened abdomen as does your specimen. Additionally, the antenna of C. marginatus is typically red-orange with black ends (as is also seen in your specimen). A more complete description from Wikipedia:

The head, pronotum and abdomen of an adult dock bug are speckled reddish brown. The antennae are composed of four segments, red-orange in colour except for the final fourth segment which is black. Between the antennae are two small projections, known as antenniferous tubercles, which can be used to distinguish this species from other superficially similar species.[6] The pronotum has angular upward facing projections and the scutellum is clearly visible. The rounded edge of the abdomen has lighter coloured markings. Adults are between 13 and 15 mm long and males are typically smaller than females but have longer antennae.

See here for an additional picture showing a specimen with less prominent abdominal markings as in your specimen.
C. marginitus tends to be found in thick vegetation, so unless you've bee around hedgerows, wasteland, or other densely-vegetated areas, it's possible you have some other closely related species.
I haven't been able to find a better matching specimen, though it seems likely I have only gotten you to the right family without being certain of the genus or species. I'll update if I can find more info...
Notes:

Your specimen does not appear to be another common hemipteran found in Poland:  Leptoglossus occidentalis, which is native to the western United States but has invaded Poland for over 10 years [Surce: Lis et al. (2008)1]

You can find a guide to this family of insects (with pictures) for the neotropics (not immediately useful to you, but a good resource) by Fernandes et al. (2015)2

 1 Lis, J.A., Lis, B. and Gubernator, J., 2008. Will the invasive western conifer seed bug Leptoglossus occidentalis Heidemann (Hemiptera: Heteroptera: Coreidae) seize all of Europe?. Zootaxa, 1740(1), pp.66-68.
2. Fernandes J.A.M., Mitchell P.L., Livermore L., Nikunlassi M. (2015) Leaf-Footed Bugs (Coreidae). In: Panizzi A., Grazia J. (eds) True Bugs (Heteroptera) of the Neotropics. Entomology in Focus, vol 2. Springer, Dordrecht


What would be the best design for spike-and-recovery and linearity-of-dilution validation experiments in one 96-well ELISA plate? I have searched in the web for a detailed explanation of doing such validation experiment, but unfortunately couldn't find a satisfactory one. I came across the following sources:

Thermo Scientific Tech tip #58: IMAHO, well written description, but still there are some issues

Pros

Clear on describing terms and straight forward calculations
Troubleshooting of the results is outlined

Cons

Not designed to be performed in one 96-well plate ELISA
No mention of any acceptable criteria for the both validation tests
No mention of blank

Quansys Biosciences: a practical design to implement

Pros

Both spike-and-recovery and linearity-of-dilution experiments can be performed in one 96-well plate ELISA
Justified introduction of the endogenous sample, which is diluted the same amount as the spiked sample
Addition of blank
Mention of acceptance criteria for both types of experiments

Cons

No mention of troubleshooting
a little bit messy plate design

R&D spike and recovery protocol: a brief one but useful

Pros

Clear on design
Mention of acceptable criteria at least for the spike recovery 80-120%
Mention of blank
Hint about possibility of using diluted neat sample until it gives reading

Cons

One sample was used for assessment and not averaging on 3 samples at least
No mention for any criteria for linearity of dilution

Issues/Questions
    - Q1: How can we combine the two experiments into one plate to spare samples, and materials?
    - Q2: Can we dilute sample with assay diluent instead of sample diluent?
    - Q3: In case low sample material is there, can we skip the neat sample and add 1:2 diluted one instead to spare material?
    - Q4: In preparing spikes in Thermo Scientific tech#58, why was it 10µl spike stock solution added to 50µl sample? what governs this addition, is there any ratio to stick to here or arbitrary ratio? Can we add 90µl sample and 10µl stock solution?

Please feel free to expand sources, or questions, and of course answers are more than welcome to achieve the following aim:

  The best design for both validation tests (i.e., spike-and-recovery and linearity-of-dilution) in one 96-well plate ELISA that will use the minimum amount of sample material as possible with explanation of calculations based on averages and clear troubleshooting plan

PS: I am short of reputation to add important tags to enhance searching, e.g.: ELISA, validation

Background:

There are a lot of recipes to extract protein from human tissues out there, but all of them boil down to one thing; preserving the tissue proteins as much as possible while obtaining a reasonable yield for downstream applications, using extraction buffer, extra techniques, and by adding protease inhibitors
ELISA is one of the those downstream applications that you might be interested in, but one important question? is the sample matrix that you have already obtained valid for the ELISA assay? keep in mind, your sample is not serum, it is a mixture of tissue, extraction buffer, and protease inhibitors, and other things as well
Two known assays are usually performed to address the above question. These are, spike-and-recovery (SAR), and linearity-of-dilution (LOD), and these two assays are specific to the analyte that you want to measure in your samples, e.g., cytokines, factors, Igs, etc...and specific also to the tissue, and assay kit as well
Often times, you are interested in performing these two assays with minimum resources as much as possible, i.e., less time, less kit materials, and, most importantly, less sample material. This can be quite challenging and it depends on many issues that is out scope of this post to discuss them all
If you are interested in performing these two assays using only one 96-well ELISA plate and examine validity of different sample matrices, sample buffer (lysis buffer or sometimes called extraction buffer) for a certain analyte, say X, then this scheme below is for you:

Technical Notes:

In this scheme, recovery is examined in 3 types of solutions; assay buffer, sample buffer and samples. These are different in their complexity. Typically, the assay buffer is usually optimized to detect the standard protein provided with the commercial kit
The idea of spike-and-recovery is that you add a certain amount from standard stock solution into the wells containing the solution to be tested (e.g., sample buffer or samples) and measure them, to see whether you can recover that amount again, and how much you can recover from it in %. If, for any reason, you couldn't recover that amount in comparison with a control well, where that same amount was added into assay buffer, then this means that something in the test solution is not in favor of the assay. The specific amount you add into the wells is called spike, and it should be the same amount across all tested wells (try to be consistent). Make sure that the added amount when diluted in the well, its final concentration should still be measured by the assay and lie inside your standard curve. E.g., if your standard curve is from 4- 4500 pg/mL, and each well has 100µl of sample, if you want now to add spike into that sample well, you may add whatever amount you want that will still give you at the end a reading inside the standard curve, you may choose to add 10µl from the highest stock which is 500pg/mL, so you end up here with 1/10, that is 50pg/mL, which is fine as it lies inside the 4-500pg/mL range. Alternatively, you can add 50µl sample + 50µl spike (500pg/mL) and would end up with 1/2 dilution (which is the same in this scheme), that is 250pg/mL, which is also fine. So it is up to you to choose, keeping in mind the final concentration should lie inside your standard curve
For the linearity-of-dilution, it is obvious that you need a high concentration solution that you can make two-fold (or whatever fold you like) serial dilution from and its reading should still lie inside the standard curve. The best candidate for this is the high spiked wells. The LOD would tell you about the effect of different dilutions on the precision of the assay
For SAR and LOD you will get at the end an average percentage from 3 samples at least (calculation example will be provided later), I added a fourth sample, but this fourth can be a different sample type, say samples from tissue culture, so it is up to you to re-design this scheme and be innovative
Choosing the best dilution is not an easy task, it is not without compromises sometimes. For example, if you have a harsh sample buffer, you may not have good recovery at 1/2, 1/4, 1/8 dilutions of the sample buffer in assay buffer, whereas almost good recovery is achieved at 1/16, then this dilution factor is most probably the one you should go for in your assay. On the other hand, 1/16 might not be detected by your ELISA assay, which is limited by its sensitivity. Here, the E wells can give you a clue whether you detect something in these unspiked samples or not, that's why I recommend you include at least one sample of high expected value of the analyte in question (this is not easy sometimes to predict) in this scheme, here this is sample 3. One more thing, if you get good recovery at 1/16 DO NOT go to 1/32 or 1/64, as it is obvious that with these higher dilutions you are reducing the chance of the analyte's detectability as it is limited by your assay's sensitivity
In most of the cases, you will see that the dilution factor of good recovery of the sample buffer in columns 3 and 4, will coincide with that of the spiked samples in columns 5, 7, and 9. This will give you the assurance that you are in the right direction. If sample 4 is extracted by a different sample buffer, then it is clear that should not expect to end up with the same dilution factor (please, be more reasonable!)


Selection of recombinant host by color selection method In recombinant DNA tech,
To select a recombinant host from non-recombinants, we have different types of techniques available.

The one I'm talking about is the color selection method with the use of 2 markers(one antibiotic resistant gene for eg. Ampicillin, and the other Z-gene).
We use Z-gene as the reporter gene.
We use vectorless E. Coli as the host cell here.

Now, when we add add Ampicillin to the petri dish containing all of the variants (transformants and non-transformants), - the non-transformants will die.
The transformants survive.

Now, we add X- gal to the replica of this petri dish, and we see some of the colonies turning blue due to the action of the enzyme β- galactosidase, which in turn is produced by the intact Z-gene in the plasmid.  That means our blue colonies are the non-recombinant ones.

My question is-

The medium taken in the petri dish should contain glucose too , shouldn't it? Otherwise the recombinants would too give the colour reaction (X-gal is a homolog of lactose) due to the Z-gene present in their chromosomal DNA (operon concept).

The question maybe silly since it's kind of obvious we have to supply basic necessities for the growth of bacteria(which obioviously is glucose).

Just wanted to confirm in case we don't have glucose available ! =p

The Z gene you are talking about should be lacZ that encodes the $\beta-$galactosidase, which is made from $\alpha$ and $\omega$ peptides. Neither peptide is functional by itself.

$\beta-$galactosidase will cleave the glycosidic bond in X-gal and form galactose and 5-bromo-4-chloro-3-hydroxyindole. The latter product then dimerizes and oxidizes to 5,5'-dibromo-4,4'-dichloro-indigo, an intense blue product that is easy to identify and quantify.

Next, you should check out the genotype of your bacterial strain because they typically have only the $\omega$-peptide encoded in its genome. Thus, the enzymatic activity of the $\beta-$galactosidase is only recovered when the $\alpha$-peptide is in the environment, and the process is called $\alpha$-complementation.

Two commonly used strains for cloning and expression in E. coli are Dh5$\alpha$ and TOP10.

The genotype for Dh5a is like this:

  F– Φ80lacZΔM15 Δ(lacZYA-argF) U169 recA1 endA1 hsdR17 (rK–, mK+) phoA
  supE44 λ– thi-1 gyrA96 relA1

Here, lacZΔM15 indicates that the M15 segment is lost from lacZ, and the mutant protein will only have the $\omega$-peptide.

The genotype for TOP10 is like this:

  F– mcrA Δ(mrr-hsdRMS-mcrBC) Φ80lacZΔM15 ΔlacX74 recA1 araD139 Δ(ara leu) 7697 galU galK rpsL (StrR) endA1 nupG

Again, you will notice lacZΔM15, which is still a non-functional peptide segment after all.

Finally, to your question. Even if the there is no glucose as primary energy source in the medium and only X-gal is present, the operon of your host bacteria(I suppose it's E. coli) cannot produce the functional $\beta-$galactosidase on its own. Moreover, the recombinants, with the vector sequence encoding the $\alpha$-peptide disrupted, will not exhibit $\alpha$-complementation. No color reaction then! :D

Reference:
1.Genotypes of Invitrogen™ competent cells - TOP10, retrieved from: https://www.thermofisher.com/cn/zh/home/life-science/cloning/competent-cells-for-transformation/chemically-competent/top10f-genotypes.html.
2.Genotypes of Invitrogen™ competent cells - DH5a, retrieved from: https://www.thermofisher.com/us/en/home/life-science/cloning/competent-cells-for-transformation/chemically-competent/dh5alpha-genotypes.html.
3. Langley, K. E.; Villarejo, M. R.; Fowler, A. V.; Zamenhof, P. J.; Zabin, I. (1975). "Molecular basis of beta-galactosidase alpha-complementation". Proceedings of the National Academy of Sciences of the United States of America. 72 (4): 1254–1257. doi:10.1073/pnas.72.4.1254. PMC 432510 Freely accessible. PMID 1093175.
4.


Why do mosquitoes not collect blood after platelets activate? This may be anecdotal...

The Indian sub-continent is in the rainy part of summer. It follows the mosquito population goes up.

So when I sliced my palm, I expected the mosquitoes to collect there in force. Yet whilst they continued to go about their business on the forearms, face and elsewhere - the blood flowing out of my palm held no attraction for them. This even after I deliberately stood still for nearly a minute! Perhaps the clotting process/platelets/etc were a repellent.

Why do mosquitoes not collect blood after platelets activate?

Blood from a cut or a wound is tainted with bacteria from the surrounding environment. To a mosquito from an evolutionary perspective it would be like eating off the floor. The blood which flows through your veins is clean(er) due to your immune system and so evolution selected a pathway based on insertion into the skin in order to obtain the meal.


Does science have an explanation of how the first "common ancestor" formed in evolution? I always have this question on my mind and I need a better explanation on this. Does Charles Darwin's theory explain it or are there any other theories which explain it better than Charles Darwin's theory?

Darwin's theory of evolution (and the modern theory of evolution) explains how the current diversity of life developed. Remember, the title of Darwin's book is On The Origin of Species, not the origin of life.

As for how the current diversity of life developed, or how species originate, the theory of evolution states that life forms change and diversify gradually, and species arise and differentiate from related species, via the processes of random mutation at the time of reproduction and natural selection. The ToE is a complex set of theories with many different semi-independent aspects but that's what it basically comes down to.

Clearly all this requires life, or imperfect reproduction at least, to exist; it says nothing about the first life, and it cannot say anything about it because given what we know of the processes that lead species to arise and life to diversify and aquire its form, those processes cannot possibly have been in play when going from abiotic stuff to the first living systems.

In other words, the Theory of Evolution is how life develops once it starts existing; it would work equally well if the first life appeared via natural chemical processes or was created by alien tinkerers or the result of a time paradoxical sandwich dropped in the wrong place on primordial Earth. The study of how life could start existing is usually called "abiogenesis".

The issue isn't actually as clear-cut as it may seem, since there is a very wide unknown space between what we consider the most archaic forms of life, and any entity that could plausibly arise via purely abiotic processes; every theory of abiogenesis does assume that a lot of the features we consider essential to life must have arisen after some kind of replication appeared, meaning those features would have evolved. So there definitely is some evolutionary biology involved in investigating abiogenesis, and maybe if we ever solve abiogenesis it will be folded into the ToE (like I said, the ToE is actually a complex set of theories and observations, not one single thing. So while our understanding of what the theory says and can say currently excludes abiogenesis, our understanding and definition of the theory could evolve). But we haven't, and it currently isn't.

You need to edit your question however, because it is completely unclear from the title or text that you are asking about abiogenesis. Your question sounds like it's about embryonic development or biochemistry. Those are the current instances we have of organisms forming; whatever processes were at work in creating the very first life, well for one thing maybe we wouldn't want to call whatever that was an "organism", but more to the point those processes cannot happen today. The atmosphere is wrong and too full of oxygen, there are organisms everywhere vaccuuming up whatever resources those original biochemical processes might have used, basically there is likely no chemical environment on modern Earth that's anything like the chemical environment life originated in.

To answer your question though, abiogenesis is currently an unsolved question, so no, Science does not have an explanation of how the first organisms formed. But if you want to have an idea of how things could have happened, what the challenges are in figuring things out, and what things Science currently considers likely or impossible, there is a lot of active research in the field and many different hypotheses. The Wikipedia page for Abiogenesis has a fairly comprehensive rundown on this.

This video describes one of them (my favorite and the first I've found actually convincing, I have no expertise whatsoever to base this on but I plug it anyway; if nothing else it gives an appreciation for what kind of things the researchers in this field look at when thinking abiogenesis) :

https://www.youtube.com/watch?v=av98Brx23_4

(disclaimer: youtube throws up an error for this video for me right now but I've watched it before, I don't know if the video's down or if the problem's on my end)


Melting point of animal fat and plant fat I notice in daily life that animal fat typically has a higher melting point than plant fat does. I wonder the reason why this happens. What exactly contributes to this difference? Is it because of the difference between molecular structure? I understand that substances have different melting point because the intermolecular forces are different. But how does intermolecular force vary between animal fat and plant fat. Is it possible for any animal fat to have lower melting point than plant fat?

Plants contains monounsaturated fats while animals contains saturated fats. The high proportions of fatty acids in animal fat means it takes longer to heat it up. I don’t know the melting points of different things off the top of my head, but you can find a meat that is as unsaturated as possible and compare it to the most saturated plant fat to test your last question.


Why not use SDS-PAGE as a method to detect viruses? Recently, I have been researching about DNA and I know the most popular method for detecting viruses is based on DNA. After learning about proteins, I wonder why we do not detect viruses based on virus proteins?

If it becomes true we can save a lot of money, instead of doing a PCR reaction, we can detect more than one disease in a single reaction.

For example, when I have the sequence of a virus from NCBI Genebank, I can know how many proteins the target organism produces and I can calculate the molecular weight of each protein. Then running it in a SDS-PAGE gel to see what the bands look like, may be that I can know the target organism is present or not?

For example, HIV produces 9 proteins and the molecular weight of each protein is different.
So after doing electrophoresis, I have 9 bands. Based on the distance between each band and based on the molecular weight, it's possible to know HIV is present or not?

Put simply, the answer is that you could seek to detect viral proteins, but because these proteins would be very minor components of your sample, you would have to use an immunoblotting technique to detect a specific viral protein. While immunoblotting is quite a sensitive technique, I think its fair to say that it can be technically demanding. In contrast a PCR reaction is exquisitely sensitive and is fairly robust. PCR is also technically more staightfoward because DNA is generally easier to work with than are proteins.

Before the advent of PCR, immunoblotting would have been the method of choice.


What is Pseudopalindrome? I stumbled upon this word in a webpage by bio.libretexts.org:

  The dam-methylase of E. coli recognizes the tetranucleotide GATC in DNA and transfers a methyl group (from S‑adenosyl methionine) to the amino group at position 6 of the adenine in that sequence. Note that GATC is a pseudopalindrome, so both strands read the same for these four nucletides in DNA.

What does it mean? How is it different from palindromic sequence?

I've searched google,ncbi and google.books but couldn't find anything.

In DNA there are four nucleotides or "bases", each of which can be matched with a complementary base on the partner chain in the double helix. Thus:

Adenine (A) and Thymine (T) are complementary and Cytosine (C) and  Guanine (G) are complementary.

So, a nucleotide sequence is said to be a palindrome if it has an even number of base pairs and is equal to the reverse of its complementary sequence.

For example, in a single strand of DNA the sequence of bases CCATTAATGG is palindromic because the sequence of bases in the complementary strand is GGTAATTACC, its reverse.

A pseudopalindrome is a DNA sequence with an odd number of base pairs yielding a symmetrical complement except at the central base-pair. For example, the DNA sequence ACCTGGT is pseudopalindromic, because its complement on the other strand is TGGACCA, which is its reverse except for the central element.

[There may be some confusion in the literature. The example cited in the question, GATC, is a palindrome, having CTAG as its complement, not a pseudopalindrome.]


Could inhibition of progerin formation slow the rate at which a body ages? According to wikipedia, progerin is activated in senescent cells. The protein itself is known to be the cause of a rare affliction 'progeria' - a disease marked by accelerated aging of the body. This disease is not accompanied by neurodegeneration.

Is progerin the key factor in the aging process?
If yes, could inhibition of progerin formation control the rate at which a body ages?

Progeria (and related) syndromes are essentially a collection of 'accelerated aging' phenotypes caused by single mutations; Progerin is a shortened version of the protein Lamin A, and is therefore not found in individuals without a loss-of-function mutation in the LMNA gene (the wiki page you reference). As far as we are aware these genes do not 'cause' aging in individuals without the mutations.

LMNA is a normal component of the nuclear lamina (a structure inherent to the nucleus). This review discusses the various diseases associated with mutations in this gene, some of which present 'accelerated aging' phenotypes. However, as far as I know, there is limited evidence to suggest that LMNA, or indeed any Lamina associated protein, is involved in 'normal aging'. A recent GWAS meta-analysis found a variant in LMNA that is associated with longevity in humans, however the association is relatively weak (OR=1.18, P=7(x10)-4), so even if this is a true association, it seems that (as usual in aging research) there are many other factors to consider, and it is not a single gene that is doing the aging.

So to stress the point: progerin has no function in 'normal' human aging - it is a defective protein caused by a germline (or novel) mutation in the LMNA gene.  Accelerated aging is the symptom of this genetic disorder, and is not completely analogous to normal aging (as you point out, there is no cognitive decline that is associated with normal human aging).


How does bone marrow acts like a valve? Wikipedia says:

  Furthermore, bone marrow performs a valve-like function to prevent the backflow of lymphatic fluid in the lymphatic system.

How can bone marrow act like a valve eventhough they neither have lymphvesseles nor contracting property?

First of all, though bone marrow is not considered a part of lymphatic system because it is not connected to lymph vessels, yet it is the site of production of both B- and T-lymphocytes and is thus considered as primary lymphoid organ1. So, it is closely related to lymphatic system.

On doing some research, I can conclude that bone marrow itself actually does not perform the role of a valve. It is the lymph vessels itself which perform the valve-like function. See this2:

  As lymph capillaries carry lymph away from the tissue spaces, they merge to form larger and larger vessels. These larger lymph vessels resemble veins, but their walls are thinner and they have more one-way valves to prevent lymph from flowing backward. Whereas the cardiovascular system has a pump (the heart) to move fluid (blood) through the system, the lymphatic system does not. It relies on the contraction of muscles to move lymph throughout the body. The larger lymph vessels have a layer of smooth muscle in their walls that contracts rhythmically to "pump" lymph along. The contraction of skeletal muscles, brought about by simple body movement, and the mechanics of breathing also help to move lymph on its way.

So, I'd consider that paragraph as one of the few places where Wikipedia has given incorrect fact.


Calculating Rate of Growth without a Population Lets say that by studying individuals of a rare species, you have determined that species gestation period, age of sexual maturity, average time between pregnancies, maximum lifespan, and average number of individuals born per pregnancy. However, you have never had enough specimens at the same time to establish a breeding population.

How can you calculate the maximum rate of growth of a population from just the information already gathered? If not, what other information would be needed?

The breeding lifespan of an individual is (maximum life span $L$ - age of sexual maturity $M$).
Call the time between pregnancies $\tau$ and the gestation period $g$. Then the average number of pregnancies per (female) individual is then $(L-M)/(\tau+g)$.
If the average number of individuals per pregnancy is $N$, then each reproducing individual produces $N(L-M)/(\tau+g)$ offspring in their lifetime.

If this species has males and females (gonochoric/dioecious), and a 50/50 sex ratio, then the number of females per female is $N(L-M)/(2(\tau+g))$.

This is a growth rate per generation: the generation time is approximately (mean time between birth of mother and birth of offspring) = $(M+(L-M)/2)$ (it's a little more complicated than this); the growth rate per unit time would be approximately equal to the ratio (growth rate per generation)/(generation time).

Other things you might need to take into account: survival of juveniles up to $M$; menopause (unusual).


Depolarisation of post synaptic neuron When the post synaptic neuron begins to depolarise as positive sodium ions move into it and it reaches threshold- does the inside of the neuron actually switch to being more positive than the outside?

I thought depolarisation meant that the inside became less negative but still remained more negative than the outside, hence having a voltage of -55mV. If the inside became more positive wouldn't the voltage be 55mV?

When the neuron reaches threshold, this is the trigger that leads to sodium channels opening and this creates a positive feedback process causing the neuron to become less negative and more positive, triggering more sodium channels to open until it is inevitable an action potential will be reached. During an action potential, the neuron cell becomes more positive compared to the outside for a very short period(ie, 1 millisecond or less).

Yes, depolarisation does mean the inside becomes less negative in this context.
You would expect the inside of the neuron to be at +55mV (or perhaps more) during an action potential, as the depolarisation of the neuron grows closer to reaching the sodium equilibrium potential which is estimated to be around +58mV. However, during the phase leading up to an action potential, potassium channels also remain open. The diffusion of potassium ions can lead to the cell becoming more negative. In other words, it limits the voltage of an action potential to around +33mV instead of +55mV.

Sources:

(1)https://www.khanacademy.org/science/biology/human-biology/neuron-nervous-system/a/depolarization-hyperpolarization-and-action-potentials

(2)https://opentextbc.ca/anatomyandphysiology/chapter/12-4-the-action-potential/


What are the physiological roles of Hydrogen sulfide? I am thinking why hydrogen sulfide has its effects in the body.
For instance, it is one Salmonella's virulence factor.
I am not sure if such a balance equations holds

H2O + H2S ←→ ...

Actually, I miss here some factors because I am not understanding the biochemistry enough to answer this.
I think H2S can exists in some sort of ionic form.
Hydrogen sulfide reminds me of ammonia.
I think it inhibits some systems.
By which mechanisms?

It is mentioned in many places the empirical effects: signaling functions similar to NO and CO.
But I am interested in how this happens.
What is the rate of adhesion of H2S to hemoglobin for instance?

H2S can change to sulfite and thiosulfate in mitochondria which are then excreted into urine.
I think most of the biological effects are done before these forms.
But in which forms?

$H_2S$ is the end product of sulfur related respirations (like sulfate respiration, sulfur respiration, etc...).

By aerob (oxygen) respiration the oxygen in $O_2$ has 0 oxidation number, by $CO_2$ the oxygen has -2 oxidation number, so it was reduced while the carbon was oxidized.

By the thiosulfate respiration of Salmonella enterica the following reaction happens by the reduction of thiosulfate: $S_2O_3^{2-} +2H^+ + 2e^- \to HS^- + HSO_3^{-}$. In this case the sulfur in $S_2O_3^{2-}$ has +2 oxidation number while the sulfur in $HS^-$ has -2 oxidation number, so the sulfur was reduced, it was an electron acceptor, just like oxygen by aerob respiration.

So in the case of Salmonella enterica $H_2S$ production is a byproduct of anaerob respiration. It makes growth faster.

  Sulfate-reducing bacteria are those bacteria that can obtain energy by
  oxidizing organic compounds or molecular hydrogen (H2) while reducing
  sulfate (SO2- 4) to hydrogen sulfide (H2S).1 In a sense, these
  organisms "breathe" sulfate rather than oxygen in a form of anaerobic
  respiration.

wikipedia - Sulfate-reducing bacteria

  Salmonella typhimurium produces H2S from thiosulfate or sulfite.

1987 - The phs gene and hydrogen sulfide production by Salmonella typhimurium.
2011 - Thiosulfate Reduction in Salmonella enterica Is Driven by the Proton Motive Force

S. enterica uses gut inflammation to enhance its sulfur related respiration to outgrow the resident microbes in the intestinal lumen (microbiota). The inflammation creates tetrathionate $S_4O_6^{2-}$ in which the sulfur has an average oxidation number of +2.5. This tetrathionate is reduced by the tetrathionate reductase into thiosulfate with sulfur having +2 oxidation number. So sulfur related respiration helps to make growth faster in order to colonize the gut.

  Here we show that reactive oxygen species generated during
  inflammation react with endogenous, luminal sulphur compounds
  (thiosulphate) to form a new respiratory electron acceptor,
  tetrathionate. The genes conferring the ability to use tetrathionate
  as an electron acceptor produce a growth advantage for S. Typhimurium
  over the competing microbiota in the lumen of the inflamed gut. We
  conclude that S. Typhimurium virulence factors induce host-driven
  production of a new electron acceptor that allows the pathogen to use
  respiration to compete with fermenting gut microbes. Thus the ability
  to trigger intestinal inflammation is crucial for the biology of this
  diarrhoeal pathogen.

2010 - Gut inflammation provides a respiratory electron acceptor for Salmonella
2001 - The Alternative Electron Acceptor Tetrathionate Supports B12-Dependent Anaerobic Growth of Salmonella enterica Serovar Typhimurium on Ethanolamine or 1,2-Propanediol

Since $H_2S$ is a gasotransmitter in the human body, there can be other mechanisms which help S. enterica.

in small amounts $H_2S$ has anti-inflammatory and anti-apoptotic effects
in large amounts $H_2S$ has pro-inflammatory and pro-apoptotic effects

So S. enterica can probably cause inflammation due to killing cells with a fast release of $H_2S$ or prevent inflammation and keep infected cells alive with a slow release of $H_2S$. I found many evidence of the pro-inflammatory theory. By the anti-apoptotic theory I wasn't so lucky, I found only a single review about anti-apoptotic strategies of intracellular pathogens, but it did not mention $H_2S$ production as a possible mechanism. So it might not be true, further studies needed...

  In the digestive system, H2S exerts potent anti-inflammatory actions,
  regulates blood flow and smooth muscle tone, modulates epithelial
  secretion and promotes healing of ulcers [4, 5].

2012 - Hydrogen Sulfide: A Rescue Molecule for Mucosal Defence and Repair

  Hydrogen sulfide (H2S) is the most recent endogenous gasotransmitter
  that has been reported to serve many physiological and pathological
  functions in different tissues. Studies over the past decade have
  revealed that H2S can be synthesized through numerous pathways and its
  bioavailability regulated through its conversion into different
  biochemical forms. H2S exerts its biological effects in various
  manners including redox regulation of protein and small molecular
  weight thiols, polysulfides, thiosulfate/sulfite, iron-sulfur cluster
  proteins, and anti-oxidant properties that affect multiple cellular
  and molecular responses.

  Understanding precise pathophysiological signaling mechanisms and the
  metabolism of H2S is a topic of active research. Unraveling H2S
  interactions within different tissues, with other biochemical
  molecules and various signaling mediators is becoming ever more
  complex.

  These results demonstrate that H2S donors can down-regulate adhesion
  molecule and proinflammatory cytokine expression, therefore
  identifying H2S, its synthesis enzymes, and molecular targets (e.g.,
  KATP channels) as potential targets for novel anti-inflammatory
  therapies.

  Thus, all of the above findings demonstrate that H2S induces
  cytoprotection by an anti-apoptotic pathway.

2013 - Hydrogen sulfide chemical biology: Pathophysiological roles and detection

  A short course of H2S infusion was associated with reduction of lung
  and kidney injury. Prolonged infusion did not enhance protection.
  Systemically, infusion of H2S increased both the pro-inflammatory
  response during endotoxemia, as demonstrated by increased TNF-α
  levels, as well as the anti-inflammatory response, as demonstrated by
  increased IL-10 levels. In LPS-stimulated whole blood of healthy
  volunteers, co-incubation with H2S had solely anti-inflammatory
  effects, resulting in decreased TNF-α levels and increased IL-10
  levels. Co-incubation with a neutralizing IL-10 antibody partly
  abrogated the decrease in TNF-α levels. In conclusion, a short course
  of H2S infusion reduced organ injury during endotoxemia, at least in
  part via upregulation of IL-10.

2012 - A short course of infusion of a hydrogen sulfide-donor attenuates endotoxemia induced organ injury via stimulation of anti-inflammatory pathways, with no additional protection from prolonged infusion

  H2S causes apoptosis in HPSCs by activating the mitochondrial pathway.
  It is suggested that H2S might be one of the factors modifying the
  pathogenesis of pulpitis by causing loss of viability of HPSCs through
  apoptosis.

2011 - Hydrogen Sulfide Causes Apoptosis in Human Pulp Stem Cells

  The level ofendogenous H2S was increasing along with the infection
  occurrence and the gradient of infection aggravate. We can presume
  that endogenous H2S participated in inflammatory reaction of abdominal
  infection and could be one of the serology index which concerned with
  the gradient of infection.

2012 - P53 The level changes and clinical significance of endogenous hydrogen sulfide of patients with acute abdominal infection

  The evidences showed that H2S has an obvious effect on colon smooth
  muscle contraction, and can increase the intestinal movements in slow
  transmit constipation. Our experiment states that H2S has
  anti-inflammation effect in prophase of acute peritoneal cavity
  infection.

2014 - P48 Regulation of hydrogen sulfide in digestive stystem
2010 - Hydrogen Sulfide Improves Neutrophil Migration and Survival in Sepsis via K+ATP Channel Activation
2012 - Hydrogen sulfide and resolution of acute inflammation: A comparative study utilizing a novel fluorescent probe
2008 - Staying alive: bacterial inhibition of apoptosis during infection

  H2S is believed to have two contradicting roles in inflammation. It
  acts as both pro- and anti-inflammatory molecule(9). Li et al.
  reported that the physiological concentration of H2S has
  anti-inflammatory effects, while higher concentrations of H2S can
  produce pro-inflammatory effects(10). The H2S inflammatory role was
  also studied in different systems. In the gastrointestinal tract, the
  H2S regulating role functions by activating KATP channels in order to
  promote the inflammation response(57). The similar H2S function was
  observed in pancreas(7), but the actual mechanisms are largely
  unknown. In conclusion, H2S pathway is a possible route for targeting
  the inflammation treatment. However, much work needs to be done for
  understanding the mechanisms of the contradictory roles of H2S in
  inflammation.

2012 - The Crosstalk between H2S and NO Signaling Pathways
2013 - Gasotransmitters, poisons, and antimicrobials: it’s a gas, gas, gas!

  Developing evidence suggests that dysbiosis (abnormal microbial
  composition or function) can contribute to if not cause chronic
  intestinal inflammation. 5,7 This inflammation can be caused either by
  an abnormal composition of entericbacteria with an elevated ratio of
  aggressive vs protective species, defective production of short-chain
  fatty acids and other protective microbial products, or enhanced
  production of hydrogen sulfide and nitrates that block butyrate
  metabolism and disrupt the mucosal barrier.

2010 - Inflammation and Nutrition in Chronic Disease
2013 - Potential Role of Hydrogen Sulfide in the Pathogenesis of Vascular Dysfunction in Septic Shock

  These results showed that physiological concentrations of H2S can
  induce apoptosis of PDL cells and HGFs in periodontitis, suggesting
  that H2S may play an important role in periodontal tissue damage in
  periodontal diseases.

2009 - Hydrogen sulfide induces apoptosis in human periodontium cells
2010 - Bacteria-derived hydrogen sulfide promotes IL-8 production from epithelial cells

  We have shown that inactivation of H2S producing enzymes
  (cystathionine beta-synthase, cystathionine gamma lyase, or
  3-mercaptopyruvate sulfurtransferase) and NO-synthase in several Gram
  (+) and Gram (−) bacteria render them highly sensitive to different
  classes of antibiotics (Gusarov et al., Science 325 (2009) 1380–1384;
  Shatalin et al. Science 334 (2011) 986–990). We also presented
  evidence that Bacillus anthracis-derived NO is critical at the early
  stage of infection (Shatalin et al. PNAS 105 (2008) 1009–1013). Here
  we show that: (1) cbs/cse and nos mutations change Bacilli global gene
  transcription profile; (2) apore formation process in cbs/cse and nos
  mutants of B. anthracis is affected; (3) virulence of cbs/cse and nos
  mutants of B. anthracis is diminished. These results demonstrate that
  bacterial H2S and NO are an important virulence factors, and that
  enzymes generated these gases may serve as an attractive target for
  antimicrobial therapy.

2014 - S7-6 Role of H2S and NO in Bacillus anthracis spore formation and virulence

Btw. there is non-hydrogen sulfide producing S. enterica too, which can probably (no study about this yet) cause salmonellosis. So using thiosulfate as electron acceptor and producing $H_2S$ might not be essential by the infection. (There are other non-sulfur electron acceptors e.g. nitrate, fumarate, etc... for the case of anaerob metabolism.)

2013 - Genetic Analysis of Non-Hydrogen Sulfide-Producing Salmonella enterica Serovar Typhimurium and S. enterica Serovar Infantis Isolates in Japan
2011 - Salmonella enterica Serovar Typhimurium Colonizing the Lumen of the Chicken Intestine Grows Slowly and Upregulates a Unique Set of Virulence and Metabolism Genes
2013 - Salmonella Uses Energy Taxis to Benefit from Intestinal Inflammation
2006 - Role of Gluconeogenesis and the Tricarboxylic Acid Cycle in the Virulence of Salmonella enterica Serovar Typhimurium in BALB/c Mice
1981 - Aerotaxis in Salmonella typhimurium: role of electron transport.
2010 - IDENTIFICATION OF NOVEL VIRULENCE GENES OF SALMONELLA ENTERICA
2014 - Increasing prevalence of hydrogen sulfide negative Salmonella in retail meats

Overall hydrogen-sulfide and other gasotransmitters are important virulence factors of many pathogens.


What is the fibre axis in the Watson and Crick paper? I was reading Watson and Crick’s original article on DNA structure in Nature 171, 737–738 (1953). The accompanying diagram (shown below) has something called the “fibre axis” going through the DNA. This axis isn’t shown in modern models of DNA, so what is it?

Short answer:
The term fiber axis is not in reference to the DNA model, it comes from the experiments that Watson and Crick referenced to guess their model (performed by Rosalind Franklin).   The fiber axis is the direction along the DNA strand.

Longer:

Watson and Crick created their model of DNA based on the esoteric experiment called X-ray fiber diffraction.  To collect fiber diffraction data ( gathered by Rosalind Franklin actually) DNA is pulled out of a cell lysate and washed with buffer.  It looks like a clear, liquid, string of snot (a technical term that is).  Its stringy though because the long DNA molecules pull out and create viscous fluid where the DNA is pulled along the length of the snot fiber.  Because the DNA is ordered in this one dimension, if you shoot a beam of X-rays through it, it creates a pattern on film that looks like this:

As you can see its got a nice X-shaped pattern.  The DNA in the fiber is mostly aligned along the fiber, in the up and down direction.  Because this is so, the spacings between the different layers is due to the spacings between the DNA bases and the x-pattern comes from the fact that DNA forms a double helix.

Some misc details - you have to use X-rays because their wavelength is about the size of an atomic bond and this is the scale of model Watson and Crick and Franklin and Wilkinson were trying to find.

The fiber axis is along the y axis (top to bottom) because the trail of DNA snot hangs down - it will sag if you hold it an angle.

Rosalind Franklin was a great experimentalist and she realized that the DNA snot trail dries out over time as the experiment would go on for days.  She set up a moist stream of hydrogen gas blowing over the DNA strand during the X-ray experiment and so was the only experimentalist who obtained what we now know to be the true result - double helical DNA.  As it dries out, DNA interconverts to the Z-DNA form I believe, which does not have the x-pattern and also confuses things because the result is a smear of the DNA helix converting from one form to another.

Francis Crick had actually predicted the X-pattern for helices.  The structure actually required these two to come together to get the answer while the American genius Linus Pauling was working hard in California on the structure as well and would have won too if he understood how to keep his snot properly damp.

The reference for nearly all of this is Watson's somewhat self-centered but historically accurate book "The Double Helix".

After some surprisingly difficult Googling, I can't found a picture of DNA fiber... picture below. You can make some yourself from the protocol listed here and some saliva, soap and other common household items.


How does a TOPflash/FOPflash assay work to detect beta-catenin protein expression? I am reading an article (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596711/) wherein a TOPflash/FOPflash assay is used to detect beta-catenin protein levels in a COS-7 cell line. I can't find a good explanation in the article, or in any other article, as to how this assay works. I understand the cells are transfected with TOPflash/FOPflash reporter plasmids, but that's about it. Any insight or redirection would be much appreciated.

From what I can understand, TOPflash is a luciferase reporter plasmid that contains two sets of 3 copies of the wild-type TCF binding regions. If the canonical Wnt signaling is activated, beta-catenin will translocate to the nucleus to associate with TCF/LEF transcription factors to activate transcription of Wnt target genes. Since this is a luciferase plasmid, you should see an increase in relative luciferase activity when substrate is added. If Wnt signaling is inhibited, you will see loss of luciferase expression. The FOPflash is used as a negative control because the TCF binding regions upstream of the luciferase gene is mutated so even if beta-catenin translocates to the nucleus to activate TCF-mediated transcription, you should not see any luciferase activity.

Hope this helps.