Can we measure the rate of mutation in (say) E. coli without gel electrophoresis or genome sequencing? If so, how? And, what are the pros and cons?

This is pretty broad question so I'm not really sure what the end goal is here, but here goes.

The answer is both: "yes" and "it depends what you mean exactly". I'll explain what I mean.

Firstly, you should clarify in your question whether what you actually mean is the substitution rate, or not. The mutation rate, which is how often a given base pair position changes, cannot be observed with any current technique, even Next Generation Sequencing. This is for 2 reasons (that spring to mind, there may be more).

If you make an observation at time $t$, and another at time $t +1$, but a base mutates (say A $\rightarrow$ C) and then mutates back again between your observations, you would not be able to tell that this had ever happened. Thus there would be 2 mutation events which you would not count in your 'rate'. This is one of the reasons molecular clocks based on SNPs tend to underestimate ancestral distances.
If a mutation occurs that is deleterious (has a negative effect on the organism), the mutation won't be observed because the lineage of the organism won't survive to be sampled. By the way, the chances of a mutation being deleterious are considerably higher than it being advantageous, but lower than it being neutral.

The substitution rate is how many mutations have occurred that persist in the lineage. Now if we assume that when you say mutation rate, you mean substitution rate...

Yes, you can study mutation rate without 'molecular techniques'.

Throughout the history of classical genetics we've studied mutation rate without access to these tools.

My favourite example is basically the one I used in this question, where you can study the emergence of antibiotic resistance in bacteria (since you provided the example of E. coli, this is rather apt).

In the papers I linked however, they will almost certainly have used some molecular techniques to validate their answers.

But, if we set that aside for the moment, the very first indication of antibiotic resistance one might observe in the lab is seeing colonies of a bacteria growing on a petri dish in the presence of an antibiotic they are supposedly susceptible to.

Now, if we consider the 'mutation rate' to be the time taken (perhaps counted in the number of generations), for a spontaneous mutation to appear as a phenotype (observed characteristic), you can assess this purely visually without any molecular techniques. If you repeated this experiment however, you would most likely not be able to verify that resistance arose in exactly the same way twice without use of various molecular technqiues.

As a molecular biologist though, I would not really consider this a very good approach/definition of mutation rate, which leads me on to...

'It depends what you mean exactly'

If you were to stick to what is probably the stricter but more widely accepted definition of mutation rate (.i.e substitution rate), you'd need molecular techniques to determine this, as you'd need to know precisely which bases are changing.

Hand-wavy list of pros and cons:

Phenotyping (pros and cons):

Quick
Cheap
Easy
Low resolution
Possibly not reproducible

Genotyping (pros and cons):

Massive resolution
Can be quick in some circumstances
Functional information
Generally expensive
Requires specialist equipment

Not an exhaustive list by any means.


Why and how does uniprot list around 150,000 proteins in the human genome? Using organism:"Homo sapiens (Human) [9606]" as a query in uniprot returns about 146,000 proteins. I was under the impression that there were only 20-25,000 protein coding genes in the human genome. Is this something to do with splice isoforms, like those from SpliceProt, or another splice isoform database or tool?

Well you are assuming one sequenced genome/proteome per NCBI tax id. That is no longer true. So if you click on the proteome filter it decreases by half.
Which gets you into the 60,000 range. Now not all of these are "different" conceptual proteins, many are artifacts from the way GenBank/EMBL/DDBJ interact with the TrEMBL section of UniProtKB i.e. they are not normalized in db speak.

So for the human case you also want to add the Swiss-Prot filter to get a decent proteome that gives you about 20,000 proteins. Corresponding to the predicted/confirmed human gene count.

In all bioinformatics databases you need to pay attention to difference between database records and biological concepts. They rarely map cleanly one to one. In this case an UniProt record is not a protein, but information about a protein and a different record could have information about the same "protein". Or at least the same under some definitions of "same".

See the announcement of the draft human proteome in UniProtKB

The known isoforms are most often stored in the alternative products section of an UniProt entry. In some rare cases when the splice variant has a completly different biological function they are described in separate UniProt entries. For UniProtKB/Swiss-Prot Human there is a near 1 to 1 relation between genes and proteins. Cases as above and fusion proteins are the exceptions to this rule.

TrEMBL tries to automatically reduce redundancy in INSDC by auto merging entries in the same taxid and now proteome that have an identical reported sequence. However, variations of single gene products due to mutations and or limit what auto merging can do. For example there are 8 records for the P53 gene in TrEMBL today. Many of them from mutants, i.e. cancer genomes etc...


Tiny dark-colored bug ID in Amman-Jordan I live in Amman-Jordan and I keep finding this bug species on my walls. I saw four till now on the walls of another room. A little bit bigger than the first one.

Click on all photos to open full-sized image:

With cm ruler:

I also have a video, but don't know how to post it.

These are very likely flour beetles (Tribolium spp) of some kind. These small (~3mm) reddish-brown beetles are some of the most widespread and common pests of stored food products worldwide [source].

 Left: red flour beetle; Right: confused flour beetle. Photo credits: Rebecca Baldwin (left); James Castner (right)
The photo is too blurry to be able to differentiate between the most likely candidates: red flour beetle (T. castaneum) and confused flour beetle (T. confusum).

You can learn more about differentiating these insects here and here, and you can find more general information about them via UF/IFAS.

Distribution: Both species are essentially found worldwide; This UF/IFAS page provides a bit more nuanced explanation of their distribution:

The red flour beetle is of Indo-Australian origin (Smith and Whitman) and is found in temperate areas, but will survive the winter in protected places, especially where there is central heat (Tripathi et al. 2001). In the United States, it is found primarily in the southern states. The confused flour beetle, originally of African origin, has a different distribution in that it occurs worldwide in cooler climates. In the United States it is more abundant in the northern states (Smith and Whitman).

Extermination tips are available via epetsupply.com:

Prevention is key!
Keeps your home clean and free of food/crumbs
Sticky traps and pheromone traps

If I had to guess, I'd guess from your poor images that you have red flour beetles, but honestly it doesn't much matter from a pest-control standpoint.

The red and confused flour beetles live in the same environment and compete for resources (Ryan et al. 1970, Willis and Roth 1950). The red flour beetle may fly, especially before a storm, but the confused flour beetle does not fly. [source: UF/IFAS]

UPDATE:
Alternatively, now that I've looked at your picture with such a small specimen, it could be possible this is another "grain beetle": Ahasverus advena, the foreign grain beetle. From Wikipedia:

 Source: Wikipedia

Description:
The foreign grain beetle is approximately 2 mm (1⁄12 in) in length. It can be distinguished chiefly by slight projections or knobs on each front corner of the pronotum, and its club-shaped antennae. The larvae are worm-like, cream-colored and often reach a length of 3 mm before pupating into darker adults. Males and females are identical in appearance both as larvae and adults. The adult is usually reddish brown, or sometimes black.

Distribution
The foreign grain beetle is found in tropical and temperate regions [and is distributed all throughout the world -- see Spanish translation of Wikipedia page].


Does night mode on iPhone really help? Okay so I know that night mode is supposed to filter out blue light that is bad for the eyes, but is it really more helpful than annoying? At night I do use it when I’m on the phone but it doesn’t make sense to keep it on during the day when it’s bright outside does it?

Different colors mean different wave lenght and energy, as displayed in the picture.

Using Planck's theory, the shorter the wave is, the more energy it carries.
On day light, all these wave lenghts are present, including UV from sun. With no sun-light, your eyes aren't hit by those, so there's no need of using higher energy waves (that's exactly how night mode on iPhone works, using only lower energy waves).


How having sickle cell trait would provide resistance to malarial parasites? It's mentioned in my textbook that subjects with sickle cell trait develop resistance to malaria. I've read a few research papers predisposing involvement of macrophages and papers asserting involvement of the heme oxygenase system rendering me confused; so what actually causes this resistance. And is this resistance also present in the subjects with sickle cell anemia? Also some African tribes are generally mutated to provide malaria resistance. See this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3499995/

I would say that there are at least 2 explanations:

Higher levels of free heme in the blood of individuals with sickle cell anaemia/sickle cell anaemia trait. Free heme is toxic to Plasmodium.sp Science. 1981 Nov 6;214(4521):667-9., detailed mechanism is described here: J Mol Med (Berl). 2008 Oct;86(10):1097-111. This effect is also observed in people with other diseases affecting stability of erythrocyte's membrane, such as thalasemia or spherocytosis.
It is also possible that, when erythrocyte's membrane is prone to disruption, Plasmodium.sp  antigenes are present in higher concentrations and may be faster presented to the immune cells.


What's the mechanism behind 'losing heat through your extremities'? I can understand how if you are not circulating enough (warm) blood, by not moving much while in a cold environment, your extremities themselves lose heat, and become cold - but I don't understand how they (the hands, feet, and head) can make the rest of your body lose heat too.

'Drawing the heat out of your body' (as people have termed it to me) doesn't make sense itself - what is the actual mechanism(s) behind the (exposed, relatively uncirculated) extremities, 'drawing' heat out of the body?

Is it that it merely draws the need to heat those (poorly insulated, circulated) extremities from the existing distribution of heating the other parts of your body, thus lowering how warm those other parts are?

If so, how does that happen? In the case above, where you're not moving the body to circulate warm blood to the hands (or using other warming stimuli like friction), how would 'heat transfer' to the hands occur then? Or does it just indeed slowly 'lose heat' and get colder and colder (which would then lead me back to my question, how would that explain the rest of your body becoming colder as a result of the extremities becoming colder)?

Your extremities lose heat at a faster rate than the rest of your body because they have higher surface area per unit volume. Heat exchange happens at surfaces, so if you have more surface, you transfer heat more quickly. Imagine you have a sphere of water with 1L volume, and a long cylinder of water, also 1L, lets say 1cm wide, the sphere will hold heat longer because it has less surface area per unit volume.

Why does losing heat through extremities cool the rest of your body? Because of your blood. As blood runs through your core, it takes heat from surrounding tissues. The blood carries that heat to the extremities, where cooler tissues pull it away from the blood. It's kind of like how the coolant in your car takes heat from the engine block to the radiator.

When it is very cold, your body will reduce blood flow to the extremities to save heat, making your fingers vulnerable to frostbite. However, it cannot stop bloodflow, those tissues still need oxygen, so you still lose some heat.


How does myopia actually work? This is potentially more or less a question about optics, but I've never been truly satisfied with any explanation that I've been given about Myopia. In fact, I almost can't even believe it. There are a million different versions of this diagram:

I understand that images of things could appear blurry when those things are focused in front of the retina, but then what discriminates between near and far things? Shouldn't everything be blurry? What exactly is different about this image when the thing being viewed is in close proximity to the eye?

The image you gave is not clear because it does not show the fact that the divergence pattern of light from a close object is different from the divergence pattern of light from a distant object.

Light rays from a close object (first image) diverge, and therefore they are in focus for the myopic eye.

Light rays from a distant object (second image) is approximately parallel, and therefore they are not in focus for the myopic eye. The lens corrects for this inability to focus and allows the distant object to become in focus.

Also note that the myopic person is still capable of focusing on close objects despite the lens because the lenses are still capable of dynamic adjustment, but less so than a person with perfect eyesight. You can test this by focusing on a near object, then putting on your glasses. The object should be initially out of focus, and then become in focus as the eye lenses adjust to the distance.

Myopia/presbyopia is fundamentally an issue of the focal range of the eye becoming limited to a specific range. If the ability of the eye lenses to dynamically adjust is further weakened, it may require progressive lenses or bifocals to correct the issue.


Bowtie: cannot read fasta file? I am trying to use bowtie2 to analyze my data in FASTA format, but it seems that this version can't read properly my data. My command line is as follows:

bowtie2 -x $REFERENCE -f $TARGET -S $TARGET.sam

The version 2 of bowtie complains with the following:

Warning: skipping read 'ORIGINAL: GACACTGTTCATGCTGGTGTCGCTGTCGGGCATTAT' because length (0) <= # seed mismatches (0)
Warning: skipping read 'ORIGINAL: GACACTGTTCATGCTGGTGTCGCTGTCGGGCATTAT' because it was < 2 characters long
Warning: skipping read 'ORIGINAL: GGCTATCTTGAAGCCAATGAGTTGTTAACTGGCAAG' because length (0) <= # seed mismatches (0)

Note that bowtie (version 1) is pleased by my FASTA! Here's a snippet and what bowtie says:

>ORIGINAL: GCTACGGAATAAAACCAGGAACAACAGACCCAGCAC
GCTACGGAATAAAACCAGGAACAACAGACCCAGCAC
>ORIGINAL: ATTAACAACAAAGGGTAAAAGGCATCATGGCTTCAG
ATTAACAACAAAGGGTAAAAGGCATCATGGCTTCAG
>ORIGINAL: GCAGAAAATGGGAGTGAAAATCTCCGATGAGCAGCT
AATGGGAGTGAAAATCTCCGATGAGCAGC

# reads processed: 471409
# reads with at least one reported alignment: 464583 (98.55%)
# reads that failed to align: 6826 (1.45%)

Now I'm at loss. Can anyone see what I'm doing wrong here? Can I trust anyway bowtie2 when it finishes and outputs how many sequences are aligned?

Thanks!

Since I apparently don't have enough reputation to comment, I'll post this as an answer and let someone move it.

Firstly, try to ensure that the order of the arguments are correct. You should be typing bowtie2 -f -x $TARGET -U $TARGET -S $TARGET.sam, since bowtie2 (as with many other programs) can be a bit picky about the argument order.

Secondly, it's usually advisable for the example input to include lines that are causing the problem (since it's apparently not complaining about the lines you posted, we can only assume that it's aligning them).

Thirdly, you'll typically only get those warnings if they're true. For example, if you were to grep -A 1 -w GACACTGTTCATGCTGGTGTCGCTGTCGGGCATTAT $target then my guess is that you'd find it to have no remaining sequence. Presumably these are the result of you trimming adapters or something like that, so just have your trimmer discard really short results (they won't align meaningfully anyway).


When does genetic randomization happen? When two parents (regardless of species) reproduce in sexual reproduction each offspring is generally a random combination of genetic traits from each parent. Their developed traits then depend on the expression of each of their genes per established genetic combinatory science. All well and good.

Now my question - when does the actual randomization of genes for a given offspring happen? Does it happen when the individual sperm and egg cells are formed, or does it happen when they combine?

So does every one of a female's eggs have the same genetics, and every one of a male's sperm have the same genetics, and when the two combine it is randomized to form the zygote?

Or is each egg unique and each sperm unique, and already "pre-randomized", and the combination to form the zygote is then a straight-forward addition?

Or is it some variation or combination of those two options? Maybe the answer actually even differs across species, or across plants vs animals, or fish vs mammals, or something?

Your view of the randomization of the parent traits seem a bit wrong and it makes the question a little unclear. But still, I think we can answer it...

The randomization happens at the moment of the creation of sperms and ovules. The two "randomizing processes" are segregation and recombination.


Why can fish survive out of water? Obviously, humans can survive underwater for a short while. I've assumed this is because at some point it benefited us to stop breathing momentarily, and so we evolved a respiratory system that was able to take short breaks.

Similarly, fish can survive outside of water for a short while. However, I can't think of a single instance for most fish where they may have needed to evolve that ability. Even their ancestors originated from aquatic environments, so I don't think it's a residual ability they no longer need.

Why did fish evolve a respiratory system that could take breaks like ours can?

Do not have too a "panselectionist" view of evolution!

You can survive in a bath of mercury for a little while. You can survive naked in the outer space for a while (see here). Yet none of your ancestors where exposed to such conditions. We can be tolerant to certain conditions without having been selected to tolerate it.

Similarly, you managed to survive in your very specific environment. Yet none of your ancestors ever encountered this specific environment.

In other words, evolution is more than just natural selection. Not every phenotype in every environment you can think of is the result of a direct selective pressure acting on it. A classical and easy to read paper on the subject is Gould and Lewontin (1979).

Why fish not die suddenly outside of the water?

The main reason why fish die outside of water is that they cannot intake oxygen from air (see Breathing under water; not considering lungfish). So once fish are exposed to air only, they stop intaking oxygen, consume the oxygen that they have left in their circulatory system and tissues and slowly die of asphyxie but there is no reason for the death to be direct and sudden.


Maximum recombination frequency During the process of crossing over, Why is the maximum possible recombination frequency between two genes equal to 50% and not more than that?

Statistically, this is that the maximum mean recombination frequency is 50%.

Recombination defined this way means that Gene A and Gene B from one chromosome are not 'together' on the same chromosome after recombination. That means that the recombination frequency is the probability of an odd number of recombination events between the loci. If there is an even number of recombination events, Gene A and Gene B end up back together again (with some rearrangement between them).

Recombination events can be modeled by a Poisson distribution: that is, recombination events are discrete (you either get an event or you don't) and they don't depend on each other. The rate can be expressed in terms of base pairs, e.g. "mean number of recombinations per base pair" or "mean number of recombinations for 'distance' X."

The probability of getting an "odd" result from a Poisson distribution is always <0.5. See for example this Q&A from Math.SE.

Spoken in plain language, let's start from two loci that are very close where the recombination rate is very low. In most cases, then, we get 0 recombination events so the genes stay together. Now, as we increase the distance, we will get more cases where 1 event occurs. However, as we increase the distance further, we will also start to get cases where 2 events occur. 2 events has the same end result as 0 events: the genes stay together. It turns out mathematically that there is no rate that you can choose where the number of "1"s is more than the combined number of "0"s and "2"s; therefore, the frequency must be <0.5, but will approach 0.5 as the rate approaches infinity. If this doesn't seem intuitive, check the math from Math.SE!


Why do cyanide and arsenic smell like almonds and garlic, respectively? Why do humans smell arsenic as garlic or cyanide as almonds? Do both smells activate the same receptor? Is there any reason why our brain interprets these smells the same?

According to CDC.gov and Toxnet, bitter almonds contain cyanide, which, gives them the characteristic odor, but this can be also due to benzaldehyde (PubChem), which is, by the way, used as almond flavor for cooking (Wikipedia).

Garlic has its odor due to allyl methyl sulfide (Wikipedia) and not due to arsenic, which is not present in garlic in significant amounts. Arsenic as such does not have garlic odor and foods high in arsenic, such as rice, chicken, fish, beer and wine (Prevention) do not smell like garlic.

However, poisoning by toxins, such as arsenic, thallium, organophosphate pesticides, selenium and tellurium (FPNotebook, PubMed) is followed by addition of the methyl group (CH3) to them by normal intestinal bacteria, which gives them the garlic-like odor.

So, the connection between the garlic odor of garlic and arsenic (or other) poisoning is in the presence of methylated substances: allyl methyl sulfide in garlic, trimethylarsine in arsenic poisoning, dimethylselenide in selenium poisoning, etc (PubMed).


Is the discovery of dominant and recessive genes the only reason Mendel matters? We've known that offspring inherit various traits from their parents since (at least) Aristotle. In The Elements of Plant Hybridization, Gregor Mendel treats that fact as common knowledge. Clearly, we don't credit Mendel with discovering it. Accordingly, it seems to me that Mendel's only notable discovery was the discovery of the existence of dominant and recessive genes. However, that discovery doesn't seem to justify the title 'founder of modern genetics', which Wikipedia, and other sources, use to refer to him.

Why is Mendel the big deal that he is?

Independent assortment. Mendel showed that his genetic markers for different traits, or phenotypes are transmitted randomly to the F1 generation. This was before the concept of linkage was discovered, so fortunately he selected unlinked genes.
Segregation of alleles. The dominant and recessive alleles segregate away from each other when the germ cells are created, therefore each parent has two copies of every Gene.
Distinguishing phenotype from genotype in a predictable and testable framework.
The test cross. It was only careful record keeping and back crosses that revealed the recessive copies of mutant alleles in heterozygotes.

One description of his contributions is available on Wikipedia.  Other sites include MendelWeb, Learn Genetics,


What percentage of individuals infected with COVID-19 don't have symptoms? There are various statistics estimating mortality of COVID-19 infections, based on how many diagnosed people have died. These numbers are used by various media to extrapolate how many people will die if the disease spreads uncontrollably.

However, what is missing here are the undiagnosed infected (due to their immune system fighting the virus fast enough and thus only presenting with mild, or no, symptoms).

Do we have any data or estimates for the percentage of infected people that are asymptomatic?

The proportion of individuals infected by SARS-CoV-2 who remain
asymptomatic throughout the course of infection has not
yet been definitely assessed.

The COVID-19 epidemic, Tropical Medicine & International health (2020)

The asymptomatic ratio is thus estimated at 41.6% (95% confidence interval (CI): 16.7%, 66.7%) among evacuees. Because fourteen days have elapsed since their departure from Wuhan—longer than the 95th percentile estimate of the COVID-19 incubation period (Li et al., 2020; Linton et al., 2020)—there is very little probability that the five virus-positive asymptomatic individuals will develop symptoms. Should one of the five becomes symptomatic in the future, the overall asymptomatic ratio would decrease to 33.3% (95% CI: 8.3%, 58.3%).

Estimation of the asymptomatic ratio of novel coronavirus infections (COVID-19), International Journal of Infectious Diseases (2020)

Our estimated asymptomatic proportion is at 17.9% (95%CrI: 15.5–20.2%), which overlaps with a recently derived estimate of 33.3% (95% confidence interval: 8.3–58.3%) from data of Japanese citizens evacuated from Wuhan [13].

Estimating the asymptomatic proportion of coronavirus disease 2019 (COVID-19) cases on board the Diamond Princess cruise ship, Yokohama, Japan, 2020, Eurosurveillance (2020)

Table S1. Model parameters. All time periods are given in days.
Parameter                     Baseline              Distribution  Reference/reason
                              (alternative values)
...
Pr(Asymptomatic | Infection)  0.178 (0.1, 0.5)      Beta          Mizumoto et al. (13) (lower, higher)

Estimating unobserved SARS-CoV-2 infections in the United States (preprint) (2020)


Are there any oxygen loving bacteria? It seems we only found bacteria that hate oxygen. Are there any bacteria that love oxygen and would thrive in high oxygen environment?

If it slowed down or stop multiplying in low (as in normal earth atmosphere) oxygen content it would be the best.

It's not true that all bacteria hate oxygen. Actually, there are some obligately aerobic bacteria that need oxygen to carry out cellular respiration. A notorious example of this type of bacteria is Mycobacterium tuberculosis, a pathogenic species that infects lungs and cause tuberculosis. Because it's obligately aerobic, in the classic case of tuberculosis, Mycobacterium tuberculosis growths are always found in the well-aerated upper lobes of the lungs where the oxygen requirement is satisfied.

Reference:
1. Levinson, W. (2010). Review of Medical Microbiology and Immunology (11th ed.). McGraw-Hill. pp. 150–157. ISBN 978-0-07-174268-9.


Impact of Natural Selection on Population Size I have conducted a lab with my IB Biology 11 class, regarding changes in allele frequencies within generations overseeing the natural selection of an advantageous phenotype. We were looking to conclude some sort of link between the changing allele frequencies and an overall changing population number of the species. Lab results saw, that as the frequency of the advantageous phenotype increased, the total population dipped and then increased after the 3rd generation. Can anyone point out any possible reasons as to why this occurred - regarding any factors at all? The image below depicts frequency of the advantageous allele vs total population.

This is pretty basic, should have learned it in year one bud, but, here... everyone should be able to decipher this.

You can also use Calculus to solve this.

Edit: The dip was most likely because natural selection often has a bit of a delay until it becomes advantageous to the population. Otherwise, the increase should continue if you go on to further generations.


Methylation Data for Erythrocytes (Red Blood Cells)? Why is it that white blood cells (leukocytes) are highly characterized in DNA methylation pure cell line profiling, but I can't find any profiles of red blood cells (erythrocytes)? Is blood considered a pure tissue type?

I'm following the deconvolution of DNA methylation data by cell type (white and red), but I can't do this without pure cell line methylation data. Can anyone help me understand either:

Why red blood cell DNA methylation data has not been purified and collected yet.

OR if it has...

Where can I access the methylation data for red blood cells (erythrocytes)?

Thanks so much for any help!!!

The answer is relatively simple: Mature erythrocytes do not have a nucleus and thus you cannot study methylation patterns there. You can do this in young, developing erythrocytes which still have their nucleus.


Are there any known plesiomorphies of all living mammals relative to a newer trait state in all living reptiles? If I understand how a "trait" is defined, a turtle's shell is a synapomorphy relative to mammals and the common ancestor of living amniotes. The same would go for a snake's limblessness, etc. But are there any synapomorphies all living reptiles have in common relative to an older trait state found in most or all modern mammals? Traits modern mammals share with the common ancestor of living amniotes which reptiles do not also possess?

The following article lists some distinctive skeletal differences in synapsids and sauropsids, and reptilia and non-reptilian amniotes:

    Sauropsida is defined as "reptiles plus all other amniotes more closely related to them than they are to mammals" (Gauthier, 1994). The characters supporting Sauropsida include the following:

  Presence of a single coronoid. Synapsids and the diadectomorph Limnoscelis have two coronoid elements. The coronoids are bones on the dorsomedial surface of the lower jaw.
  Supinator process parallel to humeral shaft and separated from it by a groove. In synapsids and diadectomorphs, the supinator process is strongly angled relative to the shaft.
  Presence of a single pedal centrale. Two centralia were present in the tarsus (ankle) of synapsids and diadectomorphs.

    Reptilia is defined as "the most recent common ancestor of extant turtles and saurians, and all of its descendants" (Gauthier et al., 1988). Characters supporting Reptilia include:

  Tabular small. The tabular (a bone on the posterolateral corner of the skull table) of early synapsids and diadectomorphs is large, but reptiles have only a small tabular, when it is present.
  Suborbital foramen present (Fig. 1B-D). The suborbital foramen is a small hole near the lateral edge of the palate, between the pterygoid, palatine, and ectopterygoid (or jugal, when the ectopterygoid is absent). This structure was not found in early synapsids and diadectomorphs (Fig. 1A).
  Supraoccipital anterior crista present. The supraoccipital of mesosaurs, synapsids, and diadectomoprhs lacks anterior parasagittal flanges. The supraoccipital of reptiles has a paired anterior parasagittal flange called an anterior crista.
  Supraoccipital plate narrow. The supraoccipital is a bone in the back of the braincase. The supraoccipital plate of mesosaurs, synapsids, and diadectomorphs is broad and extends farther laterally than the postparietal.

  Phylogeny and Classification of Amniotes, Michel Laurin and Jacques A. Gauthier


Alternatives to NCBI BLAST during US government shutdowns? Many molecular biologists are used to going to NCBI BLAST for quick, hassle-free BLAST searches of their genetic or protein sequences.

However, during the last American government shutdown in 2013, BLAST was rendered unusable due to lack of funding.

The incumbent president is also threatening to shutdown the government if funding for the Mexican border wall is not approved by the Democrats.

What are some alternatives for NCBI BLAST that are reasonably fast, easy to use, and would not be rendered unusable in the event of American government shutdowns? Ideally, the tools should encompass all of the standard BLAST sub-functions (pblast, PSI-blast, etc).

b.nota is correct - Just further adding to his answer. The International Nucleotide Sequence Database Collaboration (INSDC) is a consortium between DNA Data-bank of Japan (DDBJ), EMBL-EBI and NCBI. Contributions to each of the 3 databases are shared on daily basis.

(Thanks to @KonradRudolph) Since EMBL-EBI is not directly accountable to any single government either financially or in terms of research directions so a (temporary) shutdown equivalent to that of the NCBI is vastly less likely. Rather, like CERN, it’s an international treaty organization and thus probably a lot more robust.

BLAST

Answering part 2 of your question: YES! BLAST is available in both DDBJ and EMBL-EBI on following links:

BLAST - DDBJ
NCBI BLAST+

Scope

Here is what INSDC's website says about its scope:

  INSDC covers the spectrum of data raw reads, though alignments and
  assemblies to functional annotation, enriched with contextual
  information relating to samples and experimental configurations.

Following table (taken from INSDC website) may help you have better understanding about respective data types comparison for 3 contributors:


What is the difference between transpiration and evapotranspiration? According to my point of view transpiration and evapotranspiration are different things, but i am confused about this topic. After great effort, I found a major difference between it.

Transpiration: The loss of water in the form of vapour from plants surface is called transpiration.

Evapotranspiration: The loss of water from any surface in the form of vapour is called evapotranspiration. Such as water surface, soil and any body surface.
By educationspot

Is it correct? Please explain.

Essentially, evapotranspiration is the sum of evaporation and plant transpiration from the Earth's land and ocean surface to the atmosphere.

Here are some links to articles about transpiration: https://biolympiads.com/plant-anatomy-and-physiology/


How can a blood test give information about rickets? Can we detect rickets from a blood test? What  evidence pf rickets is in the blood and how is the blood treated to detect rickets?

From the Wikipedia article I linked to in your question:

  Serum calcium may show low levels of calcium, serum phosphorus may be low, and serum alkaline phosphatase may be high from bones or changes in the shape or structure of the bones.

There is also a rare genetic form of rickets called Vitamin D-resistant rickets or X-linked hypophosphatemia that can be diagnosed by DNA sequencing of cells collected by a blood draw.

It should be noted that, at least in the case of rickets, blood tests alone will not diagnose the disease. There are many other possible symptoms of the disease, so a patient presenting with one or more of these symptoms may also be subjected to a blood test to confirm the diagnosis, not just make it on its own.


How do humans detect temperature differentials on the skin? I just read this question on Physics SE about how the body detects cold or warm surfaces. As someone who already understands how heat flux devices like thin film gauges and thermocouples work (by exploiting the known relationship between temperature gradients and electrical/thermal properties of the relevant materials), I was actually more interested in how the nerve endings in my body actually implement this.
When I touch something warm or cold, what is the nervous mechanism that causes the correct signal to be sent to my brain, causing me to perceive a hot or cold surface?
How is the "thermocouple", which tells me whether a surface is hotter or colder than my finger, implemented?

Sensory neurons in the skin express TRP channels such as TRPV1 channels, TRPM8, and others (see Voets et al 2004 for more information on how these channels work). Different sensory neurons express different combinations of TRP channels .
Changes in temperature shift the probability of whether these channels are open or closed. Opening or closing of ion channels changes the membrane potential of the sensory neuron, which changes the rate of action potentials which informs the rest of the nervous system about the temperature.
The TRP channels can have other ligands, as well, such as capsaicin or menthol. The activity of these ligands at temperature-sensitive receptors is why we perceive chilis or mustard to taste "hot" and menthol to feel "cold".
More generally, the nervous system typically responds to changes better than constant stimuli through adaptation. Therefore, if your hand is fairly cold and you touch something warm or hot, you will perceive a hotter stimulus than if your hand started out already warm.
There isn't really a thermocouple or temperature difference detector in the skin, just these two mechanisms: channels whose open probability is a function of temperature, and sensory adaptation which heightens perceptual sensitivity to changes in temperature.

Voets, T., Droogmans, G., Wissenbach, U., Janssens, A., Flockerzi, V., & Nilius, B. (2004). The principle of temperature-dependent gating in cold-and heat-sensitive TRP channels. Nature, 430(7001), 748-754.


If I sent a bag of rice to the bottom of the ocean and brought it back, could I eat it? Suppose I filled an oceangoing container with rice and sunk it to the bottom of the ocean… say, a kilometer or so, then brought it back up.

Would it be edible?

Would it retain nutrients?

Do these things depend on how long it's been down there (at very low temperatures, mind you).

Asking for myself because, you know, I think ocean-bottom rice would be tasty.

Thanks!

Edit (after Doctor Whom's answer): I guess I should have mentioned that wrapping it in plastic is an option.  The pressure is what I was most interested in but I did a really poor job conveying that.

Depends on the container.  The bottom of the ocean has three main properties that would affect the rice:

Water
Salt and floating materials
Pressure - at the bottom of the Mariana Trench, the pressure is 1000x that standard atmospheric pressure at sea level.

Rice is absorbent.  Depending on the container, if it is permeable to water, then both seawater and pressure will affect the rice.

Rice + Water = soggy rice with a different texture than cooked rice.

Rice + Brine in Seawater = soggy rice that absorbed salt and fine particulate materials from the surrounding water.  (Cooking this would probably taste just like using seawater to cook rice.)

Rice + Intense pressure = the water, salt, and other materials would be absorbed on its way down more quickly due to the increased pressure, and any air within the grains would be replaced with water as the grain is compressed.

I do not believe it would work at all like a pressure cooker does due to the cold temperature; I am fairly certain that it would be only the grainy soggy rice - cooked rice is different from dry rice because of changes to the starches by the heat when cooking (and obviously the absorption of water).  The rice itself is a starch, so the carbohydrates would not likely respond differently to the pressure in the absence of heat.

I am curious if anyone might come up with anything on the chemistry of carbohydrates under pressure at near-freezing temperatures - whether any chemical bonds may be altered (like deformation of the beta-1-4 glycosidic linkage).  That's beyond my level of chemistry/physics knowledge.

But the duration of the journey would likely result in mush by the time it came up.  There are not many nutrients to white rice in the first place, other than the carbohydrates, so the nutrient change would be what it gains in the brine.

If I am missing something, please point it out.  But I believe this is the extent of the effects on the rice.

However:

If your rice were in a sealed container capable of withstanding the pressure without collapse or leaking, I am fairly certain that the rice would arrive back to the surface completely unchanged.  Humans are able to go down to the sea bottom in specially designed vehicles.


When DNA is at its uncondensed form, what can it do? I think it can do two things:

The cell may be duplicating the genome during S phase.
The cell may be transcribing the DNA into mRNA.

Question: Can the two activities occur at the same time or one at a time? In other words, are cells efficient multi-taskers?

At least in bacteria they can. In optimal conditions, E. coli divides itself about once every 20-30 minutes. Wich is more important, the replication time of its genome is about 40-50 minutes. That means that, in exponential phase, E. coli has at least two active replication bubbles. Since the density of ribosomes must be more or less constant, aswell that the new cells needs to synthetise peptidoglycan and other cell components, that means that replication and transcription occurs simultanously. If not, ribosomes, enzimes, tRNAs and mRNAs would be diluded in every replication event.

In eukarya I see no reason of why that shouldn't be possible. The formation of chromatin is not a random event and some specific proteins are required during short periods of time during some steps of mitosis, so it's logic to assume that some specific parts are not compacted or that transcriptional activity can occur even in chromatin.

The specific region that is duplicating itself in a given time will probably be unable to transcribe, because the polymerase complex is pretty big and they need to open the double helix, and that. But this is somehow like children playing in the train tracks. Once the train aproaches, the children stay apart, and they continue again when the train has gone.


Blue light in a fridge. Is it really beneficial or just marketing? Recently while visiting a shop with electronics I saw a fridge with a huge advertisment sticker going more or less like this:

  There's blue light source in this fridge so there will be less bacteria inside and your fruits will have larger quantities of vitamins.

Can it be true? How can dead (picked, transported and refrigerated) fruit produce more vitamins? How does blue light affect this?

Furthermore I thought that only UV light kills bacteria.

Therefore my question is: how much truth was on that sticker?

Maybe a little bit?

There are two claims here, so let's talk about them individually. I'm not sure how this light is being produced (probably LED), but it'll have a wavelength somewhere between 400 and 500 nanometers.

Reduced bacterial presence:

The intrinsic antimicrobial activity of blue light is well documented. Although the mechanism is not entirely understood and widely debated, the commonly accepted hypothesis is that the blue light triggers the production of reactive oxygen species like singlet oxygen that are highly toxic. However, this has only been observed under high-power light sources, and low levels of light may actually increase bacterial activity. What counts as a high-power source, you ask? The number from this article is $\frac{10mW}{cm^2}$. For a fridge with an internal surface area of >1 meter, such a power source should draw at least 100 W. Given that normal refrigerators use draw 100-200 watts, you'd essentially be doubling your electrical bill for the fridge.

It should also be noted that the above is a best-case scenario. As soon as you add anything to the fridge, you'll reduce the intensity and thus the effectiveness of the light source. Also, the light is unlikely to be on all the time- it probably turns on when you open the door and turns off when you close it. While this helps a lot with power use, it minimizes the effect of the blue light, which is constantly on in experiments.

Larger quantities of vitamins

There's no (reliable) evidence of light of any kind actually creating vitamins, so what the sticker suggests is that it doesn't degrade the vitamins already present as quickly as other kinds of light.

There's a good article here that discusses the stability of various vitamins. It's worth noting that most of these vitamins and essential amino acids are much more likely to be destroyed by cooking than light, which is probably why the fridge focuses its claim on fruits, which are less likely to be cooked.

There's very little research that I was able to find about the effect of different wavelengths of light on the stability of various vitamins, but as a whole I remain fairly skeptical that there's any notable difference. Most experiments that do study degradation of vitamins under light subject pure vitamins to high-intensity light for several days- unlikely to happen in your fridge.

TL;DR:

A claim like this shouldn't be a major factor in your buying decision. The effects of the blue light are probably negligible given the conditions in your fridge, but if you've got two very similar choices this feature could act as a nice tiebreaker. Besides, there's a lot to be said about how cool blue light looks and the confirmation bias present in your purchase.


Do the eyes play any role in producing the visual experiences you have during dreaming? Sometimes, you remember a vivid picture of a dream that you saw. What is the role of your eye in this experience? Please provide me with the answer that is as simple as possible since I am in Class 10(Grade 10).

Your eye doesn't play a part in your dream aside from giving you the basic images which your brain later used to form the dream. The visual image in your dream comes from your brain itself.


How are viruses weakened to be suitable for vaccination? I understand there are two kinds of active vaccination

Injecting complete viruses that are weakened to not cause the disease being vaccinated against
Injecting only antigen particles of viruses that the body creates antibodies for. So the disease can't arise, not even in a weakened form.

I am wondering how the viruses for vaccination are weakened. Is this simply a process where randomly parts of the virus DNA/RNA are taken out and tested on animals, and as soon as it is sufficiently weakened, it is considered suitable? Or is this an analytical and systematic process?

I am wondering because some popular vaccinations (including that against measles) can still (very rarely) cause fatal complications. Which made me think whether it's systematic or just "accelerated mutation and selection".

I'm interested in an answer for layman, if that is possible at all.

There is a Wikipedia page on the topic of attenuated vaccines.

Basically the idea is that the virus is grown on some sort of foreign host such as cells in culture, eggs or an animal. This selects for mutant viruses, present in the original population, which are pre-adapted to the new host (so that they grow better). By repeating this process several times it is possible to develop a new variant of the virus which grows poorly in the original host (i.e. humans) but is still able to stimulate an immune response. The resulting antibodies, will recognise a subsequent infection by the original disease-causing virus as long as the viral component responsible for the immune response is still present in the attenuated virus that is used for vaccination.


Is there a known minimal stretch of DNA that can distinguish any two people in the world? I imagine this could be used as a universal Identifier.

Here is what the data says. UK government must have had some scientific evidence when it settled on a 10 variable-length sections of genome for their database, SGM+. In one such variable sections, some people have 10 repeats of CTTT, others have 11, others have 12 etc. The largest of those fragments, at its maximum length, are about 350 base pairs. The US government uses 13 such variable-length sequences for its CIA database, called CODIS. On both sides of the Atlantic, roughly 3-4 thousand base pairs were judged to be enough, with some safety margin, by the most advanced geneticists in the world, working on public money.

The catch is that these variable length sequences are disjoint, so you end up requiring far more than 4,000 bp. If you need these markers on the same DNA strand (chromosome), you should space them by 50 centimorgans, at which distance they recombine independently. But according to http://www.sciencemag.org/site/feature/data/genomes/265-5181-2094.pdf , the longest chromosome only has 350-400 centimorgan. It means you cannot get 10 independent DNA sequences on a human chromosome, be it the longest.

I predict there is no such continuous DNA stretch, that would tell apart any two non-twins. Since it is much better to use multiple chromosomes in DNA fingerprinting, I doubt you will find more relevant experimental data.


Why use RRBS (reduced representation bisulfite sequencing) instead of general BiSeq? My understanding is that RRBS is used for certain cases. For example, WGBS (whole genome bisulfite sequencing) is limited by repeated sequences.

However, many papers seem to use both techniques.

What are the reasons researchers would use RRBS instead of WGBS?

The use of RRBS instead of WGBS is mostly about coverage vs. cost.

To confidently call methylation status at a cytosine residue, you need to have at least 10x sequencing coverage at that particular residue (ENCODE standards require at least 10x coverage for RRBS and 30x coverage for WGBS). To perform whole-genome bisulfite sequencing (WGBS) on large genomes (e.x. mammalian genomes) is very expensive if you are trying to achieve the 10x coverage requirement.

The principle behind RRBS is to improve the sequencing depth of cytosine-rich areas by enriching your sequencing library with CpG-dense regions of the genome. This is accomplished through the use of CpG-specific restriction enzymes like MspI, which recognizes 5'-CCGG-3'.

In RRBS, the entire genome is cleaved using MspI, leaving at least two cytosines per cleaved DNA fragment (one cytosine at either end of the MspI-MspI fragment). Sequencing libraries are constructed from size-selected MspI DNA fragments, bisulfite conversion is performed, and the converted library is sequenced. Specialized software is needed for alignment and analysis of the converted genome (e.x. Bismark, methylKit).

One of the major limitations of RRBS is that you will sequence only CpG-rich regions of the genome. Also, since the library is size-selected after MspI digest but before adapter ligation, you will never sequence any MspI fragments outside of your size-selection range (~40-250 bp).

I have analyzed both types of data and found that the RRBS data was very unsatisfying and didn't answer our research question. WGBS, though extremely costly, is a better option for a comprehensive cytosine modification profiling. There are publicly available RRBS and WGBS datasets at https://www.encodeproject.org/.

I must mention a critical limitation of both techniques in that neither RRBS nor WGBS can distinguish between the type of modification (methylation, hydroxymethylation, carboxylation, etc) present at a particular cytosine residue. RRBS and WGBS, which rely upon the ability of certain modifications to protect cytosines from deamination, can only be used to determine whether cytosine residues are modified or not.

Further reading:

I would suggest following this link for an exceptional technical and practical article in which the authors compared RRBS to WGBS: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4026711/

A more technical guide to RRBS: http://www.bioinformatics.babraham.ac.uk/projects/bismark/RRBS_Guide.pdf


Do local potentials always precede action potential? Do all stimuli change the membrane potential to a value lower than threshold potential first, and then by summating end up in an action potential?
How do voltage-gated ion channels detect this change in voltage and respond adequately by opening?

I have to admit that I have never thought about if lower potential stimuli can add up. I have done some research though and you are correct. If there is multiple stimuli that don't reach threshold potential it is possible that those sum up. Summation is possible due to stimuli that are directly after another or that are at the same location after another.

-> Spatial summation

-> Temporal summation

Do all stimuli have the same effects?

No - some inhibit a reaction, some provoke one.

How do channels react?
Voltage-gated ion channel contain proteins that react to changes in electrical fields .

At first the sodium channels open up when the stimuli reached treshold potential. That causes the sodium ions to rush into the cell, making it more postive. They start to close before the overshoot.

The potassium channels then start to open and repolarize the membrane.

Single shots doesn't have a huge effect on the membrane.

Na+/K+ ATPase keeps the settings for action potential alive.


Question about flavodiiron protein I came across an article about flavodiiron proteins that are responsible for reducing ${\rm O}_2$ to ${\rm H}_2{\rm O}$ thereby protecting the anaerobic prokaryotes and some eukaryotes from oxidative stress. However, I am confused about the structure of that protein and its relation to heme proteins. Is this a heme protein?

The article I am reading is:

  Di Matteo et al., The O2-scavenging flavodiiron protein in the human parasite Giardia intestinalis. J Biol Chem. 2008 Feb 15;283(7):4061-8. Epub 2007 Dec 12.

No, Hemes are not proteins. They are porphyrins (large organic molecules) which are composed of four pyrrolic groups linked together. In the middle the coordinate the iron atom which is responsible for the activity. The combination of heme and iron is called a prosthetic group or co-factor. They are bound by the protein.

The image shows the Heme B from the Wikipedia.


Are there proteins with multiple motifs? Does each protein adopt a single specific structural motif (zinc finger for example) or are there any proteins with multiple motifs along the chain?

Most large proteins contain multiple motifs; if you search online for pictures of protein structures, this should be immediately evident. Here's an example from something I was working on the other day: the WD40 repeat motif. It appears in many proteins, but those proteins are certainly much more than a bunch of WD40 units. If you investigate some of the proteins listed at the bottom of that Wikipedia page, you should be able to confirm that they are complex and made of many different sorts of domains, shapes, and parts.

You also mention zinc fingers; those are a DNA-binding motif that show up in many, many different DNA-binding proteins. Those different DNA-binding proteins have many different functions, and their specificity is handled by a vast array of different sorts of motifs and domains that sit on top of/outside of the zinc finger itself. The Wikipedia article on zinc fingers shows many different structures in which zinc fingers can be embedded, and even those structures are only small parts of the actual functional proteins that perform work in a cell.


Can people with paralyzed eye muscles see? As far as I am aware, the saccades of the eye are central to visual perception. If the eye is held still, the human stops seeing, even if light is reaching the retina and the visual pathway is intact.

But we recently had a question on UX.stackexchange about possible improvements to a visual+EEG interface used for communication with locked-in patients. The designer asking it mentioned that eye tracking devices are unlikely to work, because the patients' eyes can't move. This surprised me, as I would have thought that the patients must be able to move their eyes if they are able to read the device's screen. But I have never had contact with a locked-in person, and assume that the asker knew more about them than I do.

So, are there situations in which a human's eye muscles are paralyzed, so the eyeballs cannot be moved in their orbits, but this human still has visual perception and can mentally process information in his/her field of view?

Short answer
Visual perception persists in the absence of functional eye movement.

Background
An example case would be retinal implants wearers. Retinal implants like the Argus II consist of a set of electrodes placed onto the degenerate retina of blind folks. Electrical stimulation of the electrode array elicits flashes of light (phosphenes). Visual input is provided via a head-mounted camera, and the device translates the camera images into patterned electrode stimuli. Hence, because the camera is head worn, Argus II wearers cannot use eye movements to scan the world. They have to use head-scanning techniques. Still they are able to perceive flashes of light (phosphenes) and can recognize simple shapes and perceive motion.

In fact, eye movements such as saccades are detrimental in Argus II wearers, because the oculomotor system feedbacks muscle movements to the brain when a saccade is made to stabilize the perceptual field of view. In normally sighted people the oculomotor feedback system is important, as it tells the brain to compensate the retinal image position shift when a saccade is made. Compensation occurs through a shift in the brain representation of the retinal image to the opposite direction, thereby stabilizing the image representation. However, this is detrimental in Argus II wearers, because the position of the electrode array and hence retinal position of the image is unaffected by eye position. Hence, when subjects use their implant, any saccades will disrupt visual processing, because the oculomotor system will abberantly compensate the perceived location of the object being viewed.

More importantly, perhaps, are micro-saccades. Micro- saccades are small, involuntary eye movements. When images are present stably to the retina the images fade very quickly due to adaptive processes in retinal neurons. Micro-saccades are thought to prevent fading, as they constantly produce small, involuntary fluctuations in gaze, thereby shifting the image quickly over the retina, and thereby refreshing the retinal image and preventing adaptation (Stingl, 2013). When Argus II wearers stop scanning the image, images indeed fade within seconds (Stronks, 2013).

To get back to your question and summarize:

Title question: No, eye muscles are not needed for sight, given that Argus II wearers have sight (though artificial, crude vision). However, a functional saccade system in normally sighted folks improves scanning, and anecdotally micro-saccades prevent image fading by constantly refreshing the retinal image.

Body question: Argus II implant wearers are an example of vision without oculomotor control. Although they cannot use their eye muscles for scanning, they still have functional vision.
 However image fading is a problem in Argus II users and folks without functional eye muscles alike, so head scanning techniques will be needed.

PS: Other implant systems, such as the Alpha-IMS use light-capturing methods inside the eye. Hence these subjects can use normal eye scanning and saccades for scanning. Also, albeit anecdotally, fading is reduced in Alpha-IMS wearers, because of the micro-saccades preventing adaptation (Stingl, 2013).

References
- Stingl et al., Proc Royal Soc B (2013); 280(1757)
- Stronks et al., IOVS (2013); 54(6): 3891–901.


Neuromediator, Neuromodulator, Neurotransmitter? Of these three words, perhaps Neurotransmitter is the most obvious. I took a look at Wikipedia page for Neuromodulation and found that this is pretty similar to Neurotransmitter too. I guess Neuromediator is somewhat more broad. Could someone clarify these nomenclature for me?

Neurotransmitters were classically the most specific in terms of demands on experimental demonstration (thus, the so-called "classical neurotransmitter") but the chief role of neurotransmitter is direct neuron-to-neuron communication via the synaptic cleft in which the post-synaptic neuron has channels that readily engage the neurotransmitter.  Classical neurotransmitters also require inactivation and are stored in vesicles in the presynaptic terminal (while under the modern definition, these last two requirements aren't as strict, allowing peptides and gasses like NO to be considered a neurotransmitter).

Neuromodulators, are more of an extra-synaptic application... a bath in the extracellular medium that modulates the excitability of a population of cells.  In this regard,neurotransmitters can be considered neuromodulators when their action is on channels outside of the synaptic cleft.

I have never heard the term neuromediator before, but looking at the results on Google suggest that it is the result of translation from Easterm European languages (Polish and Romanian) and seems to be synonymous with neurotransmitter.


What is the relationship between stroke volume of blood and ventricular end-diastolic volume? I do know what each term means. That is, i know that stroke volume is: the volume of blood pumped by each contraction of a ventricle, while ventricular end-diastolic volume is: the volume of blood in the ventricle just before systole. However I can't relate the two in terms of, say, graphs or in the mode of action of the heart between this period(s).

The simplest relationship is "EDV=SV+ESV", "EF=SV/EDV" (EDV: end-diastolic volume, SV: stroke volume, ESV: end-systolic volume, EF: ejection fraction)


How many RNA-binding proteins can simultaneously bind on a single mRNA? Typically, how many RNA-binding proteins can simultaneously bind to a single mRNA?
Or said differently, how many "binding sites" does an mRNA have?
What order of magnitude?

I am interested in RNA granules like stress granules or P-bodies. They contain, inter alia, mRNA and RNA-binding proteins. I am not a biologist and I didn't come across this information so far in the related literature.

See this paper. They have studied RBP-protected sites in the entire human transcriptome by RNA-protein crosslinking followed by RNAse digestion and sequencing: PIPseq.

Figure 1 of the paper shows distribution of protein protected sites in RNAs. They also correlate it with different regions of mRNA and its expression.

They show number of protein protected sites (PPS) per transcript but that is not a proper metric in my opinion. The number should be normalized with transcript length so that you get density of protected sites. From figure 4 (see below) you can roughly estimate that average PPS density is close to 0.6 which means that 60% of any RNA is expected to be protein bound.

  Figure 4

Other points to be noted:

Highly translated mRNAs will have multiple ribosomes on their CDS and
are likely to be more protected.
Sequestered RNAs in stress granules will also have high density of PPS
Footprint of different RBPs will be different. So number of proteins that can bind to a mRNA will differ between different RBPs.

Further reading:

http://dx.doi.org/10.1186/gb4153
http://dx.doi.org/10.1016/j.cell.2012.04.031
http://dx.doi.org/10.1016/j.molcel.2012.05.021


Watermarks visible during DNA fingerprinting? Let's say we have a human man that was somewhat genetically modified from the very beginning (conception?) by a team of scientists, and is also a product of careful selective breeding. They did this hoping to produce a specimen that would  certain physical characteristics such as superior size and strength, speed, vision, sense of smell, things like that that would result in a "perfect soldier" type of man.

Is it plausible that the team of scientists, like Craig Venter's team, could have installed Watermarks in this man's DNA that would show up on a DNA fingerprint? A DNA fingerprint done by the American FBI?

A user on this forum suggested this possibility in a former thread, so I mean no disrespect to that user by asking this question. I'm just interested in feedback from others. I am writing a novel and this is research for the story. Without getting too deep into specifics, I'm trying to find a way for the authorities to become alerted to the fact that this man is abnormal from other humans.

Any input greatly appreciated.

EDIT:

Basically, I am dipping my toe into the deep end of the pool. I know only the very basics of DNA fingerprinting and Genetic engineering, so technical language is hard for me to follow. I appreciate the answers very much but I'm still a little in the dark. Another user on this forum suggested that possibly "watermarks" might show up on the test, which is why I'm attempting to rephrase the question.

I have written a scene into my novel wherein my main character, a man that has been genetically engineered, unbeknownst to him, gets into a fracas with some bad guys and he wreaks havoc and escapes. The American FBI gets some of his DNA from the scene and works up a DNA Fingerprint on him, purely for the purposes of identification if they catch him. so, yeah, just like on CSI or whatever on TV. When the technicians complete the fingerprint, they recognize that something is different about this person and they contact the lead investigator to let him know. Perhaps they see some evidence of genetic modification or something that raises their eyebrows and they feel it's worth mentioning.

So, essentially all I'm asking is if that is at all possible, and what could they conceivably have seen in the fingerprint? If it's completely not plausible then I'll either delete the scene or rewrite it.

Thanks.

The "watermarks" that you're referring to sound exactly like DNA fingerprints: stretches of DNA that are unique to an individual. These unique stretches occur naturally in all individuals, but specific artificial sequences could theoretically be inserted via techniques such as CRISPR.

Once inserted, these artificial sequences could be searched for specifically through PCR, if the sequence is known, or through traditional enzymatic restriction methods, such as described in the first link.

It's worth mentioning that in order to be easily detected, your watermarks would most likely have to be inserted into the germ line of these genetically modified humans. Otherwise, you'd only be able to get the watermark sequences into a small region of tissue. Once in the germ line, the body's own DNA replication mechanism takes over copying those sequences throughout the organism.

Good luck writing!


What is this insect found in a shower? I hope the picture is clear enough, I've found a worm like insect like the one below a little while ago in my shower, and today I found another one. I've never seen something like this. I would say it is slightly bigger than a centimeter.

Location: Netherlands

Why do they come in my shower ?

It is a species of silverfish such as Ctenolepisma longicaudata or Lepisma saccharina for examples (thanks @RHA for correction in comments).

Silvefish are well known very resistant pest typically found in washrooms and sometimes in kitchens. They are not directly dangerous but can cause property damage. Here is a webpage giving advice on how to get rid of them


Pectinase Enzyme Assay I am working on pectinase enzyme assay. I incubated 900 ul of substrate for 10 minutes in the water bath, followed by adding 2ml of DNSA reagent, then 100ul of enzyme extract added finally i read the absorbance @ 540 OD. However the values are high. How can I troubleshoot high enzyme blank values in Pectinase assay ?

So, your blank is everything but the enzyme? That is, substrate and DNSA with 100 uL water? If yes, measure, as negative controls, substrate alone and DNSA alone. If one of them is also highly absorbing light, it may be contaminated, and a new vial should be ordered. If both are highly absorbing, it may be the water you are using, or the spectrophotometer.

Alternatively, you may try to measure a time course. If blank's absorbance is increasing as time goes by, there is contamination, and reordering reagents may help you. If absorbance stays constant, you are not looking at an enzyme contamination, that is, the culprit is spoilt water, or broken spec, or even wrong protocol. (That is, reordering or repeating won't help.)


What is this and is it dangerous? Is this some type of moth, it looks dangerous is it?
I have only seen something like this once before.
Thank you for any information you can give me.

That's a wheel bug (Arilus cristatus), a species of assassin bug named for the wheel-shaped projection on their thorax. They tend to prey on pest insects, but they do "bite" humans with their proboscis. The result is an extremely painful, itchy welt, though non-venomous.

These one's don't attack unprovoked, however, so generally just when trying to handle them. You should handle them with gloves.


What are the effects of combining rapamycin with dietary restriction? Are the effects additive or subadditive? In many ways, rapamycin acts like a CR mimetic, but even CR can only go so far.

To clarify; administration of rapamycin (a drug) to lab organisms (including mice [1]) extends lifespan. Similarly, restricting the intake of nutrients to the minimum without causing malnutrition also extends lifespan in lab animals (including primates [2]).

Rapamycin inhibits the mTOR pathway (mammalian Target Of Rapamycin) - specifically mTORC1 (Complex 1) - which influences protein synthesis, autophagy and inflammation (among others). Upstream factors of mTOR include nutrient availability and insulin signaling (see "Deconvoluting mTOR biology" for good review [3]).

It has been hypothesized that the lifespan-extending effects of caloric restriction (CR) are mediated by mTOR (one can see why - mTOR is affected by nutrient availability). In fact it may depend on the method of CR;

Greer et al [4] report that different methods of CR in C.elegans, for instance feeding them a diluted food source, or conversely feeding them on alternate days, do not necessarily require the same genetic pathways. Not only this but CR combined with a genetic mutant (eat-2) have additive lifespan-enhancing effects.

So whilst the evidence is not concrete, and I look forward to other studies in mammals similar to the one by Greer et al, it looks as though rapamycin and CR have similar but not exactly the same effects on lifespan; rapamycin specifically inhibits an individual pathway which is involved in many processes, and some of its effects are not necessarily desirable (e.g. rapamycin inhibits the immune system [5]). On the other hand, CR (most of the different types) seems to be mediated by mTOR - this difference is critical: mTOR is not necessarily inhibited by CR, it is just required for its effect.

Therefore combining rapamycin and CR is unlikely to have an additive effect as rapamycin may override any influence CR has on mTOR signaling, but I have not seen a study in which this has been tried. Combing different methods of CR (or developing drugs to do just that) may well have additive lifespan-enhancing effects.

Harrison DE, Strong R, Sharp ZD, et al. Rapamycin fed late in life extends lifespan in genetically heterogeneous mice. Nature. 2009;460(7253):392-5.
Colman RJ, Anderson RM, Johnson SC, et al. Caloric restriction delays disease onset and mortality in rhesus monkeys. Science (New York, N.Y.). 2009;325(5937):201-4.
Weber JD, Gutmann DH. Deconvoluting mTOR biology. Cell cycle (Georgetown, Tex.). 2012;11(2):236-48.
Greer EL, Brunet A. Different dietary restriction regimens extend lifespan by both independent and overlapping genetic pathways in C. elegans. Aging cell. 2009;8(2):113-27.
Thomson AW, Turnquist HR, Raimondi G. Immunoregulatory functions of mTOR inhibition. Nature reviews. Immunology. 2009;9(5):324-37.


How exactly is casein digested? I mean it seems first step is rennin or pepsin digestion in stomach - then what happens with remaining peptides?
I am interested in the whole process from casein to amino acids.
Is there brush border enzymes involved in the small intestine or all process is in the stomach?

Casein proteins are soluble in milk but form insoluble curds once they reach the stomach, making it hard for digestive enzymes to break them apart. Slower digestion also is associated with delayed release of the protein's amino acids into the bloodstream.

milkgenomics.org/article/dairy-protein-digestion-life-slow-lane/

These properties of milk caseins may have evolved to benefit mammalian infants, but slowed digestion offers the benefit of increased satiety to milk drinkers of all ages. Eating foods, like milk, that take the slow lane may mean eating less food overall.

Casein proteins in milk form small spheres, called micelles, with the hydrophilic (water-loving) portions of the protein on the outside of the sphere and the hydrophobic (water-fearing) portions on the inside. With hydrophilic structures on the outside, the micelles are soluble in water (or milk, which is mostly water) [1,2].

But when the micelles reach the stomach, “one of the most ingenious events in nature takes place” [2]. The digestive enzyme chymosin snips one of the bonds on the exterior protein (known as the kappa subunit), leaving only the hydrophobic subunits inside [1]. Without their protective layer, the now insoluble proteins form a curd.

It looks like various proteolytic enzymes digest the casein 'curds' in the stomach and intestine.  "Human proteolytic enzymes were obtained in the
activated state by collecting human gastric (HGJ) and
duodenal juice (HDJ)" This is the article: In vitro digestion of bovine and caprine milk by human gastric and duodenal enzymes
Dipeptidyl Peptidase IV's  (DPP IV), a type of protease, has been shown to break down the proteins in gluten and casein. https://www.livestrong.com › Diseases and Conditions

It's in our intestine: https://www.ncbi.nlm.nih.gov/pubmed/7522442

Brush Border Enzymes & casein [that one gives me your stackexchange question!]
This article: "Effect of diet on enzymes of the brush border of the small intestine and kidney of rats" says: "Diets with low starch and high casein contents resulted in higher specific activity of leucineaminopeptidase in the small intestine than diets with high starch and low casein contents."
You can find out a bit more about that enzyme by reading the abstract of the article.
'Digestion of peptides in small intestine' in Google gives this: "The brush border of the small intestine is equipped with a family of peptidases. ... They function to further the hydrolysis of lumenal peptides, converting them to free amino acids and very small peptides. These endproducts of digestion, formed on the surface of the enterocyte, are ready for absorption."

www.vivo.colostate.edu/hbooks/pathphys/digestion/smallgut/absorb_aacids.html

[Hint - it's google searches all the way, with an occasional scholar.google search.  ... Maybe I should get back to my own work and let you all do the searches!]


What are the factors to consider when determining the sample size for a given study? Say I'm designing a retrospective study (where I'd collect data from various schools for the last 5 years) to see if consuming milk can contribute to childhood obesity.  How do I decide on how many schools to visit? If I remember my stats correctly, in general, the goal is to achieve 95% confidence in our results, right?  So how many schools would I have to collect data from so that I will have 95% confidence in the outcome of the study?

Could be as much as possible – using multistage sampling. But it all depends on how much you are willing to spend, and your time constraint.


Is Plasmid pGLO a stable or unstable plasmid varient ? Is plasmid pGLO a stable or unstable plasmid varient?

The pGLO plasmid uses a stable version of GFP. This is stated in the pGLO education series protocol, and wiki.

I could however, engineer to be unstable if wanted.

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


Do I have to chew for digestion to kick in? Liquid nutrient-rich products (such as Soylent) are consumed without chewing. But if I have to chew to initiate digestion, are those nutrients really "processed"?

If you had to chew to digest, then beverages like sugary sodas would never be digested or provide calories or nutrients, as you (generally) don't chew when you drink them. No, chewing is not required for digestion or nutrient absorption. Chewing is important when eating solid foods, as the chewing action breaks down and begins to solublize the food, and stimulates the production of saliva, which contains enzymes that begin to break down the food prior to digestion in the stomach and intestines.


Do all different types of neurons serve different roles? I know from my basic education in neurology that the brain has various sorts of neurons. These are usually bunched into 3 different categories (sensory, moto and interneurons).

I read in a recently published book, and papers on modern neuroscience that there have been thousands of different types of neurons identified in the brain. Does this mean that there are different types neurons each dedicated to a very specific task in the brain? If that is true, then what is each individual neuron's job (a few examples would be sufficient)?

Short answer
Neurons were (and still are) often identified based on their histological features (e.g., by Cajal). In turn, the structural hallmarks of neurons are often related to their specific functions.

Background
The question is broad and difficult to answer without restricting to some example types of neurons. As you say, about 10,000 types of neurons have been identified. Their roles are often obscure. I will restrict the answer below to a few examples of neurons with relatively well characterized histological features and relatively established functionality.

Fig. 1. Examples of neuronal cell types. A. Purkinje cell B. Granule cell C. Motor neuron D. Tripolar neuron E. Pyramidal neuron F. Chandelier cell G. Spindle neuron H. Stellate cell.source: Ferris (2012)

The Purkinje cell (Fig. 1A) receives large amounts of input in the cerebellum, integrates it and sends it away to deeper layers. Hence, as an integrator, it has an elaborate input side (large dendritic tree) and a single output axon. The basic  function is similar to the pyramidal cell in the cerebrum (Fig. 1E) and their appearance is hence similar.

On the other end of the spectrum is the spindle neuron (Von Economo neuron, Fig. 1G), which is believed to receive simple input and generate simple output and is built for speed. Less integration allows for faster responses. Hence, its dendritic tree is much less elaborated than the Purkinje cell (cf. fig. 1A) (Allman et al., 2011).

As a last example: the Chandelier cell (Fig. 1F); these neurons have axons that form elaborate collaterals that are believed to form local inhibitory connections in the cortex to keep (excessive) stimulation in check; hence their output is more elaborate, with relatively simple input. Dysfunction is believed to be associated to epilepsy (excessive stimulation) (Inan & Anderson, 2014).

References
- Allman et al., Ann N Y Acad Sci (2012), 1225: 59–71
- Inan & Anderson, Cur Opinion Neurobiol (2014), 26: 142–48
- Purves D et al. (eds.) Neuroscience, 2nd ed. Sunderland (MA): Sinauer Associates (2001)

Source
- Ferris, 2012, Sci Am blog


Time required to evolve advanced chromatophores in octopuses and squid? Do we have any idea how long it took primitive Coleoida to evolve from non-color changing organisms to color changing organisms?  Granted, not all coleoidans can change color (vampire squids are good example), many of them do.

(Coleoida is the subclass below Cephalopoda that includes all squid, cuttlefish and octopuses.  Nautilus' are excluded.)

Here is a print screen from oneZoom.org.

Coleoida include decapods and octopods, both of which have chromatphores, so their MRCA (which lived 330 millions years ago) probably did as well. Coleoida is a sister group to the nautiloids. They branched +400 millions years ago. Together they form the group of cephalopods. As nautiloids do not have chromatophores, the evolution of chromatophores probably occurred in between these two nodes (between MRCA of cephalopods and MRCA of coleoida). In other words, it occurred at some point during a period of about +70 millions years.


What specie of flying insect is this? The insect pictured below just flown into my room. I live in Central Europe (Poland), it is about evening now. The thing is about 1,5 cm in length (not sure about this, I was too focused on driving it out). Its white stripe on abdomen seemed to be translucent. What is this insect?

It's a pellucid fly, a species of hover fly. scientific name: Volucella pellucens
https://www.naturespot.org.uk/species/pellucid-fly


Definitions and examples of some math-releated ecology branches I would like to have an example of application and a brief description/definition (two or three lines) of the following fields. I would like to understand the exact differences between them. Other related informations are also extremely appreciated e.g. if these are fields in growth, the name of the best researcher in that field, best institution etc.

Computational Ecology;
Mathematical Ecology;
Numerical Ecology;
Statistical Ecology;
Ecoinformatics.

Although work in those areas is definitely all related, there are some kind of general differences in how those labels tend to be used, and I'll take a stab at defining them:

Mathematical ecology - this is typically the creation of theoretical models composed purely from math (i.e. not stochastic computer models). Examples include a lot of classics from ecological theory, such as Lotka-Volterra models of predation and competition, but there are also people who still do this kind of research, such as Peter Chesson in his research on the storage effect.

Numerical ecology - this is not a term that I've heard used very frequently, but I think it tends to cluster pretty closely with mathematical ecology, perhaps with more of an emphasis on also including and analyzing empirical data. I hear it used more to refer to techniques than actual ongoing areas of research.

Statistical ecology - I think this term gets used more loosely because obviously statistics are important to most ecology research. It can either refer to research that makes heavy use of advanced statistics because the questions that its getting at are hard to untangle from other effects, or research that uses a statistical model to make its point (note that statistical models are generally different from the mathematical models mentioned above in that their goal is generally to determine how likely something is to happen rather than to untangle some fundamental principle of ecology). A lot of studies on neutral vs. niche-based community assembly would probably fall into the category of statistical ecology. Here is one of many examples.

Ecoinformatics - maybe this is just because I study ecoinformatics, but I tend to think that this is the most distinct of the fields that you mentioned, although it certainly still has a great deal of overlap with the others, especially since it's a pretty diverse subfield. In general, ecoinformatics focuses on making use of large datasets in ecology. This involves both research on developing methods for doing this (for example, I study ways to efficiently collect information from ecological wireless sensor networks. Another good example is the development of GIS tools) and research that uses these methods (e.g. a study that uses GIS to synthesize sensor data and observations of a given organism to determine what that organism's range will be as climate change progresses, or that otherwise seeks to pull ecological concepts out of the data).

Computational ecology - I left this until last, because I think it's the vaguest of the labels you listed. It definitely includes ecoinformatics, but it probably also includes a lot of statistical ecology (and perhaps numerical and mathematical ecology too). I think that the main reason that it's a useful label is that it can catch areas of research that don't really fit in to the other labels. For instance, I once saw a study on quantifying niche space using support vector machines. It was really interesting, and maybe it could be classified as ecoinformatics or statistical ecology, but it didn't really quite fit into either of those. So I guess I tend to see computational ecology as a catch-all term.

These are just the impressions that I have gotten - if others chime in too we can probably build a better consensus definition of these labels.


How does the stem-loop cause intrinsic transcription termination? In this animation, towards the end (about three quarters) the process of transcription termination is shown. It states that the transcribed RNA forms a hairpin loop (or stem-loop), which halts the transcription process.

My question is, why does it halt the transcription process, considering that the RNA polymerase moves in the opposite direction of where the stem loop is created? Does it somehow change the RNA conformation such that no further bases can be added? Interpreting it as a physical obstacle doesn't seem to make any sense here.

There are two mechanisms of transcriptional termination in prokaryotes.  The one shown here is "rho-dependent" because it involves rho, a DNA-RNA helicase that loads on and unwinds the RNA from the DNA, terminating the elongation by the polymerase.  Check out [1] which shows a model for how rho multimers move through the RNA.

The other mechanism involves just a hairpin. The paper [2], especially Page 23, part C, shows how "rho-independent" or "intrinsic" termination works.  Basically, the hairpin slows down the polymerase and destabilizes the transcription bubble, allowing the intrinsically-weaker A:U bonds to fall apart.

There is no requirement for a hairpin in rho-dependent termination, and I think the movie is mixing them up.

 Geiselmann J, Wang Y, Seifried SE, von Hippel PH. 1993. A physical model for the translocation and helicase activities of Escherichia coli transcription termination protein Rho. Proceedings of the National Academy of Sciences of the United States of America 90: 7754–8. [pdf]
 Datta K, von Hippel PH. 2008. Direct spectroscopic study of reconstituted transcription complexes reveals that intrinsic termination is driven primarily by thermodynamic destabilization of the nucleic acid framework. The Journal of biological chemistry 283: 3537–49. [pdf]


What differentiates diseases like Covid-19 and Polio from the common cold Why are vaccines required for our body's immune system to destroy viruses that cause the likes of Covid-19 or Polio, while viruses that cause the common-cold are self-limiting (go away on their own)? What is so different about viruses that cause diseases requiring vaccines?

There is not really an inherent difference between these viruses.  Polio is a run of the mill enterovirus - some of its closest relatives are "common colds", while others are less pleasant - see https://www.slideshare.net/TarekMahbubKhan/enteroviruses-and-polio for some examples.  Note that some "common cold" viruses have uncommon but nonetheless devastating polio like effects; a leading culprit for acute flaccid myelitis (polio-like paralysis) was the common cold enterovirus D68 ( https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(18)30094-X/fulltext but I haven't checked for updates lately).  But for that virus, damaging replication in nerve tissue is at most a rare complication rather than a frequent one.

Coronavirus has long been known for several strains of "common colds"; they were just not as frequently deadly.  Unfortunately, we did not see the "cold and flu season" as a demonstration of defenselessness against viral outbreaks, and did not use the opportunity to practice exterminating them.


Why there is a very high drop in pressure from arteries to arterioles? Laplace law explains why the pressure is the same in aorta and arteries (100).
I am thinking why there is so big drop in pressure when going from arteries to arterioles (40-60).

Why there is a great drop in pressure from arteries to arterioles?

The vessel diameter is the most principal determinant to control resistance. Compared to other smaller vessels in the body, the artery has a much bigger diameter (4 mm), therefore the resistance is low.

In addition, flow rate (Q) is also the product of the cross-sectional area of the vessel and the average velocity (Q=AV). Flow rate is directly proportional to the pressure drop in a tube or in this case a vessels, although there are other factors of blood vessels that contribute towards the difference in pressure drop in bifurcations of blood vessels. These include viscosity, length of the vessel, and radius of the vessel.

Factors that determine the flow's resistance as described by Poiseuille’s relationship: ∆P=8µlQ/πr4:

∆P: Pressure drop/gradient µ: Viscosity l: length of tube. In the case of vessels with infinitely long lengths, l is replaced with diameter of the vessel. Q: flow rate of the blood in the vessel r: radius of the vessel

Assuming steady, laminar flow in the vessel, the blood vessels behavior is similar to that of a pipe. For instance if p1 and p2 are pressures are at the ends of the tube, the pressure drop/gradient is (p1−p2)/l =∆P.

In the arterioles blood pressure is lower than in the major arteries. This is because velocity of flow is increased with decrease in diameter and vice versa.

Source: http://en.m.wikipedia.org/wiki/Blood_pressure_drop_across_major_arteries_to_capillaries

This is important as for efficient exchange at the capillary bed pressure and flow need to be much lower.


Garden Mushroom Identification Could someone please identify this mushroom?
Found in a garden situated in a mild Western European country.

Looks like shaggy ink cap, Coprinus comatus, to me.

Blacksmith37's answer suggests that shaggy mane is the usual common name. I hadn't heard that name until I looked at the Wikipedia page. In the U.K. it is shaggy ink cap, inkytop, inkhorn or lawyer's wig.

Update

This is a good general source of information. Also comatus (Latin) means hairy.


What neuro-motor diseases cause the lower esophageal sphincter (LES) to malfunction? Please note: This question is neither homework nor seeking medical advice. I'm simply asking for a factual, objective, biological explanation of the various neuro-motor diseases/illnesses that can act as the underlying cause to LES malfunction.

The primary function of the lower esophageal sphincter (LES) is to prevent stomach acid from backwashing into the esophagus. This sphincter is an involuntary muscle, and so, for it to malfunction (unable to fully or properly close), it must be the result of an underlying neuro-motor (autonomic) disease or condition.

What such condition attacks this sphincter/valve, thereby causing it to malfunction and not operate properly? How exactly does this condition effect the sphincter biologically/neurologically?

Update

Looks like the Vagus Nerve (10th Cranial) innervates this sphincter, so I guess the question is: What neuro-motor diseases attack the Vagus Nerve or cause it to malfunction?

This is called achalasia. According to UpToDate, the mechanism for this diseases are generally unknown. What is known, however, is that the esophagus has a neural system called the myenteric plexus and if these ganglion cells in the esophagus are damaged in any way (e.g. physically, followed by Wallerian degeneration, or the primary process of degeneration after physical damaging of neurons), it can lead to lower esophageal dysfunction as these neurons regulate the inhibition of the contraction of this sphincter muscle. Dysinhibition leads to a closed sphincter.

Yes, you are right in that the vagus nerve is the primary route of the myenteric plexus to the central nervous system, so damage here might result in dysfunction as well.

Histological studies have reported fewer myenteric neurons in people with achalasia, and inflammatory cells in the region, perhaps suggesting infection or autoimmune etiology 1.

Additionally, from the UpToDate article, Chagas Disease has been associated with this disease. Chagas disease is a parasitic disease caused by the species Tropanosoma Cruzi, and these parasites multiply within cells, causing them to burst.

Check out pathophysiology of achalasia on websites such as UpToDate.

1 "Histopathologic features in esophagomyotomy specimens from patients with achalasia." Goldblum JR, Rice TW, Richter JE. Gastroenterology. 1996;111(3):648.

EDIT:

I answered the opposite, but the principles still apply. Here is a wonderful resource on this topic ("Physiology of esophageal motility," http://www.nature.com/gimo/contents/pt1/full/gimo3.html. It includes a diagram showing the vagal neural pathway and the main neurotransmitters responsible for each action (relaxation and contraction).


Is there any conclusive study relating the food consumed and the occurrence of acne? The internet says a million things about what to eat and what not to eat in regards to impacts on acne. For instance:

Refrain from dairy products.
Refrain from food heavy in unsaturated fat.
Refrain from too much sweet.
Consume fresh food (raw fruits & vegetables) but no cabbage and cauliflower.
No Alcohol
Etc.

My question is:

Is there really any relation between food consumed and the occurrence of acne?

The short and unsatisfying answer is no-- it remains controversial due to lack of high quality randomized clinical trials. According to an article in UptoDate, a reliable resource for many physicians, last updated September 2014, there is an association between acne and intake of milk in which milk components could exacerbate acne. Unfortunately, there have been no randomized clinical trials on this subject. According to the same article, "there is no reliable evidence that ingestion of chocolate is associated with an increased prevalence or severity of acne." In a similar light, the article continues on to say that "data on favorable effects of dietary factors such as zinc, omega-3 fatty acids, antioxidants, vitamin A, and dietary fiber on acne vulgaris are limited. Further studies are necessary to determine the roles of these supplements in acne vulgaris."

Reference:

http://www.uptodate.com/contents/pathogenesis-clinical-manifestations-and-diagnosis-of-acne-vulgaris?source=search_result&search=acne+and+food&selectedTitle=1%7E150#H8


Does all the citrus fruit contain Citric acid and Ascorbic acid? While reading a sixth class book about acid bases and salts. I figured that that citrus fruits like lemon, orange etc.. contains citric acid. But in the same book they also given that amla contains Ascorbic acid. Amla being a citrus fruit should contain Citric acid. I am just confused with this.

  Just tell me whether all the citrus fruits contains both citric acid as well as ascorbic acid.

I checked in wikipedia & also in oxford dictionary.

Whatever the colloquial/vernacular/etymological meaning of "citrus"; when it comes about scientific names; Citrus is a particular genus. It do have many species.

  "Amla being a citrus fruit"

No. Amla (Phyllanthus emblica) is not a member of genus Citrus; not even allied.

Ascorbic acid is just another name for Vitamin C. It is also present in common edible citrus fruits.


Why do chameleons move back and forth? I was always curious, why do chameleons have this strange gait?

The movement you observed serves two functions:

Imitation of leaves to protect against predators
Improved stereoscopic vision while scanning for their own prey

Imitation of leaves (mimesis)
Chameleons in the wild live in trees and are surrounded by leaves. In order to protect themselves from predators they move forth and back to blend with leaves moving in the wind.
Also note that their torso shape resembles a leaf:

Why do they move like this even when there is no wind and they are not sitting on a tree? I suppose they just follow their instincts. Evolution "did not prepare" them for sitting in a cage. The lack of ability to know when to move and when not was not a evolutionary disadvantage so there was not pressure to get rid of it.
Improved stereoscopic vision
Chameleons are predators that use their tongue to catch prey e.g. grasshoppers. While they are looking for their next target, they scan their surroundings with both eyes independently, i.e. one scans the left hemisphere, the other eye scans the right hemisphere, thus during this time they have no stereoscopic vision.
Moving forth and back helps alleviating this. They can estimate the distance to their distance better through the use of motion parallax (closer objects seem to move more than object further away when we move sideways). Once they found a target they turn in its direction and then use both eyes to focus on it, preparing to shoot out their tongue.
(Disclaimer: I am not a biologist. This is from my own reasoning and the German Wikipedia article about Chameleons)


Relation between goose bumps and temperature As we all know, cold weather will cause us to have goose bumps. I honestly don't know why (1), because our skin contracts?

Apart from that something quite contradicting happened this morning. I was taking a hot shower and it was so hot that I suddenly felt that I had goose bumps. Not because it was cold, but because it was so hot. How can this happen? Because of a sudden change in temperature the skin goes haywire? Or aren't goose bumps related to temperature in a way, but is a sort of safety reflex?

Goose Bumps (a.k.a. - Goose Pimples) are caused by the Arrector Pili muscles in your skin:

Their purpose is to increase the distance from epidermis to the top of the follicle, and increase the area between follicles. This has the effect of increasing the amount of air trapped between the hair and surface of the skin. In other mammals the end-result is an increase in the insulatory properties of their fur, meaning they will stay warmer or cooler depending on their current needs.

Another function in our mammalian cousins is to simply appear larger, and thus more of a threat to any predators or dangerous animals. Much like the shoulder and lower back hair on this dog:

Thermoregulation in humans has evolved since our furrier ancestors; we sweat to cool off, and shiver to keep warm. We also use tools and weapons, can create fire, and have other ways to communicate our lethal capabilities.

Goose Bumps are the human body utilizing old instinctual reflexes in the proper situations, but we lack the thick mattes of hair our ancestors had for the reflex to have any significant effect. They're a fun Easter-egg, a leftover that doesn't do us any harm and are an easy way to tell if someone is cold or scared - which might be useful under the proper circumstances.