What are the functions of disulphide bonds?

Disulphide bonds occur in proteins, not amino acids, although they involve a covalent bond between two amino acids (both cysteine).

The received wisdom is that disulphides are used as extra stabilisation of the structure of proteins which are secreted, or which have an extracellular domain. It's important to get hold of the idea that they do not occur in the cytoplasm, but are only formed in proteins which pass through the secretory pathway: they are formed in the endoplasmic reticulum (ER), and there are resident ER proteins (protein disulphide isomerases) whose function is to assist in their formation.

Classical examples of disulphide-bonded proteins are insulin (where the A and B chains are linked by disulphides) and immunoglobulin G where each Ig domain has an intradomain disulphide, and where the heavy chains are linked by disulphides. There are, of course, many others.

Cells also contain the tripeptide glutathione which includes a cysteine residue. the ratio of oxidised (disulphide bonded dimers) to reduced (monomers) glutathione helps to set the redox state of the cytoplasm and the lumen of the endoplasmic reticulum.


Tackling the second part of the question first: If a wasp is stung by another wasp, that's usually super bad for the wasp in question. Wasps are pretty good about not stinging one another, but occasionally wasps from other communities come in and cause a ruckus, or even predate on other communities of wasp specifically. If a wasp gets stung by one of these, it's about to die horribly, then get eaten.

On the other hand, if it's stung by 'friendly fire', it'll just die horribly. The venoms wasp stingers carry, while merely irritating and only occasionally fatal due to allergies on our scale, are generally pretty lethal to insects, arachnids, and other tiny critters; also, having a huge hole in your exoskeleton doesn't help.

As for the attraction question, the answer is a solid and absolute 'Eh, probably not.'.

Wasps, like a lot of insects, communicate on pheromones and dancing, but on the whole their 'deal' when not hunting is to repel, not kill. They don't care if what they sting gets killed or not; so long as it gets out of their zone of control. While they do issue alarm pheromones and other calls to action, these are not associated with stings in particular, which mostly deliver poison and sharp force trauma, not orders to the swarm.

You'll probably want to clean out the stings in any case, but it's unlikely that your new house guests want anything so much as just going home. Usher them out the door, and they'll be happy as clams.


Is resource partitioning a type of character displacement?

Does it look like character displacement?

By the fact that these two species feed at different moment of the day, they therefore have slightly different ecological niches. It is indeed the type of consequences brought about by character displacement. Yes, it looks like character displacement.

"Resource partitioning" is not necessarily more behavioural than anatomical and even if it was, a behaviour is a phenotype, just like any other phenotype, and it should not be disregarded. The character being displaced in a 'character displacement' scenario can be behavioural. So, yes if two species evolve to prey at different time of the day to avoid competition, then they have evolved so as to reduce the overlap between their ecological niche and we can call that character displacement.

Is it character displacement (highlight on a few missing information)?

It is possible (likely) that they evolved to feed at different times as a reaction of their competition and hence it would be called "character displacement" but technically speaking the question does not explain how these two species had been diverging in their feeding. It is possible that divergence in their feeding time happened long before being found in sympatry. In fact, the question does not even make clear that the two species are found in sympatry.


How hard would it be to create a protein "by chance"?

In the original column for The Claremont Review of Books, David Gelertner does not suggest starting from atoms, but from amino acids. This changes the calculation slightly:

  The total count of possible 150-link chains, where each link is chosen separately from 20 amino acids, is 20^150. In other words, many. 20^150 roughly equals 10^195, and there are only 10^80 atoms in the universe.

In any case, these kinds of estimates are purely theoretical and are not hugely useful. We do not know how early proteins evolved, but they did not have to just assemble from scratch.

As mentioned in the comments, this kind of argument for creationism (or 'Intelligent Design') is like a card trick - you start by dazzling with vast numbers, and use them to conceal the logical sleight of hand.

The premise of his argument is simple - there are a vast number of possible sequences, only a small fraction of those can fold into functional proteins, and there have not been enough mutations to make up the difference.

There is this strange argument:

  But what does generating new forms of life entail? Many biologists agree that generating a new shape of protein is the essence of it

I'm not sure who these 'many biologists' are, but the relationship between novel folds and new species is not clear to me, at least.

Anyway, the second part of his argument relies on the work by Douglas Axe on estimating the fraction of functional folds (see this paper for example). Although he describes him a bit oddly ("Axe is a distinguished biologist with five-star breeding") it's reasonable to make this kind of estimate.

  He estimated that, of all 150-link amino acid sequences, 1 in 10^74 will be capable of folding into a stable protein. To say that your chances are 1 in 10^74 is no different, in practice, from saying that they are zero. It’s not surprising that your chances of hitting a stable protein that performs some useful function, and might therefore play a part in evolution, are even smaller. Axe puts them at 1 in 10^77.

So here is the very small number to contrast with the very large one of the first step. Now for the 'bridge' - the large number of attempts that would be necessary to make a very rare event (a folded, functional protein) possible.

  Suppose, then, that every bacterium that has ever lived contributes one mutation before its demise to the history of life. This is a generous assumption; most bacteria pass on their genetic information unchanged, unmutated. Mutations are the exception. In any case, there have evidently been, in the whole history of life, around 10^40 bacteria—yielding around 1040 mutations under Axe’s assumptions.

So the argument - roughly - is that 10^-77 * 10^40 is still very small. That is, mutations are not frequent enough to overcome the extreme rarity of functional sequences.

The sleight of hand, I think, is to confuse abiogenesis and mutation. When talking about the entire 'landscape' of possible sequences we are talking about abiogenesis - randomly picking 150 amino acids (say) from an alphabet of 20. When talking about bacteria we are obviously talking about mutation.

We really have no idea how the first primordial proteins formed, or what their properties were. They could have used a smaller set of amino acids (although this does not change the numbers much), or could have assembled from multiple smaller peptides, or even been partially folded.

On the other hand, mutation of existing proteins necessarily happens on sequences that can already fold. Moving to a sequence that is a neighbour in fold space is very different to picking a completely new point in that space.

So really, the numbers do not tell us anything because they relate to separate questions.


A program for cell motility assessment with a batch process function?

ImageJ has several tracking plugins, a good one being TrackMate. Most of it's functions can be scripted in various languages and the Fiji distribution can also run in headless mode. It's open source and won't cost you any mony for a much lager feture set.

I personally have used ImageJ in headless mode scripted with its own macro language because it is relatively easy to learn.
TrackMate also should output average speeds for the tracks, if I remember correctly. Otherwise you would have to write a script to measure those from the tracking data. You can use the IJ macro language, Python, Java or one of the other supported languages.

In combination with a bash script wrapper for its headless mode I even use it in Makefiles to convert my tiff stacks to avi and put scale bars and time stamps on everything.

Hope this helps.


Currency metabolites vs. current metabolites: What's the right term?

Currency refers to anything that is used in any circumstances, as a medium of exchange [1]. That's why ATP and NAD are considered as currency metabolites [2]. So currency metabolite can be used for any metabolite that has multiple uses in different reactions/pathways.

Current refers to something that is prevalent at the present time [3]. So current metabolite is used to refer a metabolite that is already available for a specific reaction/pathway and doesn't need to undergo supplementary transformations to fit for that specific reaction.

The same metabolite can be simultaneously a currency metabolite and a current metabolite for a specific situation.

References:

Wikipedia contributors, "Currency," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Currency&oldid=611672968 (accessed July 12, 2014).
Gerlee P, Lizana L, Sneppen K. Pathway identification by network pruning in the metabolic network of Escherichia coli. Bioinformatics. 2009 Dec 15;25(24):3282-8. doi: 10.1093/bioinformatics/btp575. PubMed PMID: 19808881.
The Free Dictionary by Farlex. http://www.thefreedictionary.com/current


What are the effect of microtubule or microfilament inhibition on yeast expression profile?

Browsing around GEO, I see 13 experiments focusing on microtubule disruption in yeast.

This CHIP-CHP experiment actually uses nocodazole.

This is a microarray experiment with benomyl treatment.

The rest focus on specific mutants that try to perturb the microtubules in specific ways.

What's more if you broaden the search there is an extensive body of work including human cell lines work as well...


Evolution of protein and protein efficiency

A few details

  One of these species, species A, is close to the common ancestor of A and B, in terms of evolutionary distance, while B is farther although for both cases, it took two speciation events to end up with species A and species B.

I have two issues here.

I don't understand why this information matter for your question.
There are several metrics of evolutionary distance. In terms of time to common ancestor and therefore, in terms of number of neutral substitutions (it is ok if you don't understand why I talk about neutral substitutions) species A and species B are at exactly the same "evolutionary distance" to any of their common ancestor. However, you may want to talk about evolutionary distance in terms of "By how many standard deviations of a quantitative trait did the mean trait value shifted since the common ancestor (in haldanes unit by definition)", then one species might be more closely related to the ancestor indeed. But in such case, you need to talk about the quantitative trait resulting from protein changes and not directly at the discrete, non-ordinal (nominal) nature of proteins.

And a third general issue I have

As I understand the question, I don't think the question is specific to proteins at all. The question seem rather to relate to "environment specific adaptation in comparative genomics and reaction norms" and would be completely legitimate to look at that at the level of a protein or of a quantitative traits.

To answer your question

You are interested in the measure of fitness as a function of both environment and the protein under consideration. The relationship between the fitness (and other quantitative traits) and the envrionment is referred to as the reaction norm.

Here the graph display the quantitative trait (could be fitness) in the Y axis and environment in the X axis (as it is usually represented).There are two lines, for two different genotypes (the two different proteins in your case).

  Can we show that the protein evolved to a degree to suit the different environment of species B compared to species A?

Well, looking at the graphs it looks like indeed one protein has been under selection in one environment while the other has been under selection under the other environment. Testing this is just a matter of statistics. Basically, to test for this, you run a linear model with the quantiative trait (eventually fitness) as the response variable and the environment, the genotype and their interaction as explainatory variables. If the interaction term is significant (and if the directionality of the interaction is the one you would expect, that is genotypes are more fit in the environment where they live and if each genotype outcompete the other in at least one environment), then the genotypes are locally adapted.

EDIT

  what counts as significant?

You can chose the level of significance that you wish (0.05 for example). If this is unclear, you'll probably want to learn more about stats before.

  can you provide an example of when this method you have described was used the literature to show the evolution of a protein?

If you want example from the literature you can just type Genotype by Environment Interaction on google scholar and will get tons of hits. Here is a paper discussing this methodology specifically and here is a (old) book on the subject. I am not sure why you're still talking about proteins. Most often those studies are done at the level of the gene (or directly on the phenotypic trait). But you can find the gene and get the protein sequence from it or even play around to visualize it with various biophysics softwares.


Pump and transporter are synonymous: they refer to proteins that, unlike channels, use a form of active transport to move ions or molecules against their concentration gradient, although "pump" is most often used in the context of primary pumps, that is, those that directly use ATP, whereas "transporter" is more often used to describe the whole category or secondary pumps that use existing gradients.

  then also iam still confused why sodium potassium pump is in the category of ion transporter but not in ion pump

I have no idea where you are getting this statement from, clearly the sodium potassium pump is a pump.

Gadsby, D. C. (2009). Ion channels versus ion pumps: the principal difference, in principle. Nature reviews. Molecular cell biology, 10(5), 344.


Confusion related to the use of PCA to determine the background network

I am by far not an expert, but I read the paper and maybe I can help clarifing things a bit.

Let's start with the simplest answer to your question:
In the last paragraph of the Introduction paper the authors say

  "Throughout this manuscript [...]'background networks' and principle components are used interchangeably." ([1] Torkamani and Schork, Genetic background and drug response, The Pharmacogenomics Journal (2012) 12, 446-452; doi:10.1038/tpj.2011.35)

So they did not "use" PCA to get the background networks, they just call the PCs background models to indicate how they interpret it: As stated earlier in the introduction

  "...interacting networks cannot be expected to correlate strongly with drug response, as their influence may only be observed when the major determinant of drug response and the interacting network complement one another or are both at a synergistic state. A major problem with identifying these interaction partners [...] is the extremely large number of possible partners [...] and [...] that individual genes are unlikely to accurately represent the overall state of a biological network." [1]

As far as I understand the article, they suggest PCA as a kind of compromise: Ignoring interactions would miss associations of all networks lacking a single gene representing the network's state accurate enough. Including all interactions is infeasable due to the huge number of gene-pairs. By PCA, the number of interactions can be decreased by orders of magnitude while keeping a maximum on information (as in variation): Instead of using the interaction (as in product) of all probes with all probes, they only consider those of all probes with the first six PCs.

I think, in this context 'background' is not used in the meaning of 'background noise' but of 'cultural background' - instead of assesing individual interactions, genes are assigned a 'background'. Since this corresponds to a) the biological network(s) they belong to and b) the principle components(s) they contribute to, those two ideas are used synonymously by calling PCs 'background networks'.


Do human genes get affected by irregular sleep and other factors

This is a good opportunity to correct some major misconceptions. I'll be brief and avoid being technical because this is introductory biology.

First, genes are present on DNA, and "store instructions" on building proteins, among other things. Poor diet, lifestyle and sleeplessness do not primarily affect the DNA itself, but rather the reading of it and the production of the proteins. Genes seldom get lost or damaged in a way that affects the next generation, at least in modern humans. Analogy: genes are the recipe in the cookbook, not the prepared dish. Lifestyle choices affect the dish.

This is because the aforementioned "bad habits" must affect cells responsible for the next generation (sex cells) - which is unlikely - unless the effects of the "bad habits" are strong enough to influence the entire system and cause damage to the production or maintenance of sex cells or their DNA. Sex cells are well isolated from the rest of the body. The other foreseeable way these habits can affect the next generation is to affect pregnancy itself. Poor sleep or smoking during pregnancy is obviously not advised. Gestation is a critical period in development.

In short, the expression and action of genes is certainly affected by sleep, diet, and so on, but the genes themselves are much less affected. Mutations may build in the body and contribute to the formation of cancer and other disease, but the sex cells specifically are very likely to remain mostly unaffected; it is these cells' DNA that is passed down to children.

As for the I have some relatives of mine with really good genes that are worth passing down* statement... That's a matter of eugenics and short-sighted opinion, which is strictly not scientific. Let's not address that!


Generalities

There are plenty of ways at looking at phenotypes that affect the fitness of the carrier and of other individuals. One of them is group selection and another one is kin selection. Those two concepts are just two different ways of looking at the same processes. Now let's consider only the kin selection way of looking at these processes.

You can either consider the impact of the phenotype of a focus individual to neighbour individuals or the impact of neighbour individuals to the focus individual. Looking at it both ways, would yield to count the effect of your phenotype on twice. It doesn't make much sense to talk about the mean inclusive fitness of a population. You can only talk about the mean fitness of a population.

The confusion

The reason for all these confusion boils down to what $B$ and $C$ really mean. One of the issue is that you confuse $B$ and $b$, $C$ and $c$. The formulation $rB>C$ is a oversimplification of the reality. Hamilton did not use this formulation at first and interpreting $b$ as the benefit for the carrier might be misleading. It is important to understand Hamilton's rule in its original formulation and it is important to understand the evolutionary game theory that underlies the evolution of social traits.

What is Hamilton's rule

One cannot study the evolution of social traits under the kin selection framework if (s)he doesn't understand the underlying game theory. $rB>C$ assumes that the game we're playing is the Prisoner's dilemna. You can learn more about game theory. You can learn more about evolutionary game theory on wiki or in this book. Here is a Khan academy video on Prisoner's dilemna

Let's assume we are playing prisoner's dilemna. The fitness of an individual which cooperate is by definition $w_o + b - c$ (note the letters are not capitalized). If you cooperate and the other don't, your fitness is $w_o - c$. If you don't cooperate and the other does cooperate, you fitness is $w_o + b$. If nobody cooperates, your fitness if $w_o$. And by definition , $b>c$. Knowing the frequency of people that cooperate in the population $y$ and knowing and your probability of cooperating is $x$. Then, the level of altruism (frequency of cooperations) increases in the population if and only if

$$R\cdot\frac{dw(x,y)}{dx}>\frac{dw(x,y)}{dy}$$, where $R$ is the coefficient of relatedness which can itself be expressed as a correlation between the variables $x$ and $y$. $w(x,y)$ is the fitness of the the individual being altruistic with probability $x$ in a population where individuals cooperate with probability $y$ and $\frac{dw(x,y)}{dx}$ is the partial derivative of the fitness function with respect to $x$. By definition, $\frac{dw(x,y)}{dx} = B$ and $\frac{dw(x,y)}{dy}=C$ (capital letters).

The mean fitness of the population therefore depends on the frequency of cooperation $y$. Let's assume for simplicity that $y=1$ (equilibrium), then the mean fitness of the population is $w_o + b - c$ (note that the letters, $b$ and $c$ are not capital letter), and the variance in fitness is null. All individuals has a fitness of $w_o + b -c$ as all individuals are altruistic and perform action that has a negative impact on the fitness $-c$ and a positive impact on their fitness $b$.

In short

$b$ and $c$ in your question, correspond to $b$ and $c$ in my answer and not to $B$ and $C$. If you're playing prisoner's dilemna, then by definition, if everybody cooperate (no variance in the population), then everybody has a fitness of $w_o + b - c$ and the mean fitness is $w_0 + b - c$ (as there is no variance). Now the question of whether everybody ends up cooperating depends on $B$, $C$ and $R$.

In your edit, you write $rb$ and $c$ but you get confused about the meaning of $b$ and $c$. If you are playing prisoner's dilemna, when you cooperate with someone that is also cooperating, you inclusive fitness is $b-c + r(b-c)$ and if you cooperate with someone that is not cooperating, your inclusive fitness is $b-c + r(b)$.


What is this blue-green bioluminescent jellyfish I saw at Aquarium of the Pacific?

That is a Jellyfish! :D

Someone else took a picture of that same Jellyfish:

http://www.yelp.com/biz_photos/aquarium-of-the-pacific-long-beach?select=36BuiiqeN7OIFbowSDkPcw

Here is a picture from an article about the exhibit's jelly fish:

Source: New Jellies Exhibit at Aquarium of the Pacific Explores the Mysterious Lives of These Gelatinous Sea Creatures


How the concentration of an antibiotic is chosen for YPD medium?

According to this site,
for yeast (I assume this means Saccharomyces cerevisiae) you should use 50 µg/ml to 200 µg/ml; for fungi (!) use 100 µg/ml to 300 µg/ml. The site also stresses the importance of the pH of the medium.

I think that, unless a Hansenula expert comes along,  you will have to try an initial experiment to measure the sensitivity of untransformed cells across the range indicated. Then you can try selecting resistant cells at a concentration somewhat higher than that which kills untransformed cells. Finally, you can check to see how resistant the transformants are, to enable you to decide on a useful concentration for routine selection of transformants.


What's the meaning of the label MRE and a number like 162 or 600 in the names of bacteria?

MRE is an acronym for the Microbiological Research Establishment at
  Porton Down, UK.

It was applied to Escherichia coli strain MRE600 as that was where the strain was first deposited, according to this paper.

I tracked the answer down in an article by Chris Morris on the Culture Collection Page of Public Health:

“My association with Porton Down, the current location of the European Collection of Animal Cell Cultures (ECACC), started at an earlier date than the inception of ECACC, and was when the site was known as the Microbiological Research Establishment (MRE), part of the Ministry of Defence.”

The numeric portion of the strain designation (600 etc.) that follows MRE is presumably just a reference or accession number within the institute, with no biological meaning.

(As a matter of interest, Porton Down had a certain notoriety in Britain back in the ’60s as a secret military establishment.)


How does Golgi's neural histological stain work?

Some background information.

First of all one should notice, that Golgi staining belongs to so-called morphological types of stainings in neuroscience, where the actual anatomy of different neurons is revealed (compared to other techniques, like Ca-imaging or potential imaging).

Second, Golgi staining is a type of silver staining, there the sedimentation of silver or its salts (here: silver chromate) reveals the morphological traits of the cels.

And, third, Golgi staining is applied to fixed preparation. This means that the tissue (normally a brain slice) is pre-treated (here: with formol) to kill all cells and arrest every biological process.

What is known about the targets.

The common description of the target is quoted as "a limited number of cells at random in their entirety". This is the essence of Golgi staining:

Only single cells are stained, therefore there is no impediment from adjacent cell staining while deriving the morphological structure of the cells (very important for light microscopy where you have integrated input from different depths).
The cells are stained randomly, there is no known preference among neuronal cells for Golgi staining and I haven't seen any other types of cells in CNS stained with Golgi, therefore it is quite specific for neuronal cells (and leaving macro- and microglia, astrocytes etc. intact).
The cells are stained in their entirety, meaning that the complete cell is stained very nicely, showing detailed arborisation of dendritic tree, that was very important in studying of Purkinje cells in cerebellum.

Are larger neurons more likely to be stained? Are specific cell types more susceptible than others?

Golgi staining is used mostly for brain slices (I have never seen or heard its application for other tissues). Traditionally one of the biggest cells here are pyramid neurons (NA, ACh-ergic) and one of the smallest are interneurons (often GABA-ergic) -- both are amenable to Golgi staining (reference) and there is no seemingly clusterization of stained cells by their size or transmitter type.

What is preventing us from using the advanced molecular biology techniques to understand the process?

I can name several reasons for this:

Since Golgi staining is applied to fixed preparation the tissue is already "damaged" (formol leads to dessication of cells and shrumping), therefore it is difficult to use some fine mollecular biology methods to investigate these tissues.
There is no way to tell which cells get stained beforehand. And as long as  the microcrystallisation of silver chromate is started it can't be (easily) stopped and reversed. Therefore it is difficult to look at what caused the staining afterwards, then the whole cell is impregnated with silver.
I think there were no real attempts to crack the mistery of this staining: how intersting it might be, this seems to be an interdisciplinary question on the brink between biology and chemistry. So, maybe one day somebody will look into it and explain everything.


One easy way to make an animal faster (especially if it is larger than a housecat), is to make the ends of the limbs lighter, the more mass there is near the end of a limb the more energy it takes to move it and the slower you can swing it, that translates into moving slower because you cannot get the limb back into position for the next step fast enough.

Because of this reduction in the mass and number of toes in lower limb is an adaptation we see over and over again in animals focusing on running speed. We see it in dinosaurs, we see it in ungulates and artiodactyls. We see five toes reduced to three then eventually one toe, or sometimes we see a reduction from four toes to two paired toes instead.

Source


"Curated" is mostly synonymous with "manually curated", which means that these genes have been experimentally validated. Most non-curated genes are just predicted by a software.


First you need to identify your ant, for Czech Ants: http://www.antweb.org/taxonomicPage.do?rank=species&project=czechants&images=true

How should I feed and keep an ant queen?

Home for Pet Ant, Ant Farm:

There are lots of things you can use, for example, a clean transparent glass or plastic jar, or a fish tank of a size which you will decide is best for the ants you're keeping in it. As long as the container provides enough space, and the addition of any air holes small enough to prevent the ants escaping (much easier said than done); and also so you can observe your ants going about their daily activities, then it should be fine! Worker ants like to forage, so your set up needs to allow for the ants to do a spot of hunting for their food.

It is possible to make your own type of "Ant Farm" by using lengths of wood or plastic which have 2 grooves cut into them, like the frame used in double glazing. As long as you can place the frame onto a sturdy base to prevent it from falling over; or you can use plaster and other materials such as aerated concrete blocks, better known as Ytong nests. Two panes of clear glass or plastic can be placed into the grooves and sealed. Use the silicone sealant that is used around baths or sold where you buy glass fish tanks, but do remember to let it set and dry out well, as this will allow any chemicals to disperse harmlessly into the air before you add any ants. Also make sure that you can safely access your ant home, so you can put food in etc. You can also check out this youtube video or Wikihow.

Always try to cover your ants when not observing them to exclude light, as for most of their lives ants live in underground nests or places well away from daylight. This does not mean that they won't tolerate light; but they prefer to be in total darkness if possible, and queens rarely come out from their nests in the wild.

Feed the ANT:

If you are using a  gel-filled ant farms, it  contains all the water and nutrients your ants need for survival. Make sure to keep your kit sealed so the gel does not dry out.

In sand-filled ant farms, you need to add a few drops of water and small bits of food every few days. Ants also love a special treat of water with sugar dissolved in it, but this can’t take the place of fresh water for drinking. You can provide them with a bit of honey at times, and they will probably drink some of that. A small section of meal-worm can help provide her with a protein boost. Again, feeding them until the first workers arrive is not necessary as they do not forage during this period naturally.

Moreover, Interesting Links:

http://askabiologist.asu.edu/collecting-queen-ants

http://ant-farm-stores-review.toptenreviews.com/what-you-need-to-know-about-ant-farms.html

www.tarheelants.com/

Also, try "Ants can be pets" group on Facebook.


Does vitamin C decrease after reacting with oxygen free radicals?

Correct, vitamin C (ascorbate) acts by donating 1 electron to a free radical (reducing them to a stable compound with paired electrons), and is thereby itself oxidized to semidehydroascorbate. This is actually a radical itself, but can be reduced back to ascorbate by thioredoxin reductase or cytochromes, using NADH or NADPH as the reducing agent. A pathway diagram with references is found here.

So to answer (1), ascorbate is continuously recycled after neutralizing free radicals, and is therefore not consumed to any large extent. Therefore, vitamin C is only needed in the diet to replenish the small fraction that is lost from the body (about 1--3% per day; see this book).

And yes, vitamin C is very important in defense against free radicals; it is considered the major water-soluble antioxidant in humans.


What is the sequence of pPROLar.A plasmid?

The pPROLar.A112 sequence is:

  CCATGGGTGA ACAGAAACTG ATCAGCGAAG AGGATCTGGG TGGAGATGAC GATGACAAGG
  TGGTCGACAA GCTTGGATCC CTGCAGGCCT CAGGGCCCGA TCGATGCGGC CGCTTAATTA
  ATTAATCTAG AGGCATCAAA TAAAACGAAA GGCTCAGTCG AAAGACTGGG CCTTTCGTTT
  TATCTGTTGT TTGTCGGTGA ACGCTCTCCT GAGTAGGACA AATCCGCCGC CCTAGACCTA
  GGGGATATAT TCCGCTTCCT CGCTCACTGA CTCGCTACGC TCGGTCGTTC GACTGCGGCG
  AGCGGAAATG GCTTACGAAC GGGGCGGAGA TTTCCTGGAA GATGCCAGGA AGATACTTAA
  CAGGGAAGTG AGAGGGCCGC GGCAAAGCCG TTTTTCCATA GGCTCCGCCC CCCTGACAAG
  CATCACGAAA TCTGACGCTC AAATCAGTGG TGGCGAAACC CGACAGGACT ATAAAGATAC
  CAGGCGTTTC CCCCTGGCGG CTCCCTCGTG CGCTCTCCTG TTCCTGCCTT TCGGTTTACC
  GGTGTCATTC CGCTGTTATG GCCGCGTTTG TCTCATTCCA CGCCTGACAC TCAGTTCCGG
  GTAGGCAGTT CGCTCCAAGC TGGACTGTAT GCACGAACCC CCCGTTCAGT CCGACCGCTG
  CGCCTTATCC GGTAACTATC GTCTTGAGTC CAACCCGGAA AGACATGCAA AAGCACCACT
  GGCAGCAGCC ACTGGTAATT GATTTAGAGG AGTTAGTCTT GAAGTCATGC GCCGGTTAAG
  GCTAAACTGA AAGGACAAGT TTTGGTGACT GCGCTCCTCC AAGCCAGTTA CCTCGGTTCA
  AAGAGTTGGT AGCTCAGAGA ACCTTCGAAA AACCGCCCTG CAAGGCGGTT TTTTCGTTTT
  CAGAGCAAGA GATTACGCGC AGACCAAAAC GATCTCAAGA AGATCATCTT ATTAATCAGA
  TAAAATATTA CTAGATTTCA GTGCAATTTA TCTCTTCAAA TGTAGCACCT GAAGTCAGCC
  CCATACGATA TAAGTTGTTA CTAGTGCTTG GATTCTCACC AATAAAAAAC GCCCGGCGGC
  AACCGAGCGT TCTGAACAAA TCCAGATGGA GTTCTGAGGT CATTACTGGA TCTATCAACA
  GGAGTCCAAG CGAGCTCTCG AACCCCAGAG TCCCGCTCAG AAGAACTCGT CAAGAAGGCG
  ATAGAAGGCG ATGCGCTGCG AATCGGGAGC GGCGATACCG TAAAGCACGA GGAAGCGGTC
  AGCCCATTCG CCGCCAAGCT CTTCAGCAAT ATCACGGGTA GCCAACGCTA TGTCCTGATA
  GCGGTCCGCC ACACCCAGCC GGCCACAGTC GATGAATCCA GAAAAGCGGC CATTTTCCAC
  CATGATATTC GGCAAGCAGG CATCGCCATG GGTCACGACG AGATCCTCGC CGTCGGGCAT
  GCGCGCCTTG AGCCTGGCGA ACAGTTCGGC TGGCGCGAGC CCCTGATGCT CTTCGTCCAG
  ATCATCCTGA TCGACAAGAC CGGCTTCCAT CCGAGTACGT GCTCGCTCGA TGCGATGTTT
  CGCTTGGTGG TCGAATGGGC AGGTAGCCGG ATCAAGCGTA TGCAGCCGCC GCATTGCATC
  AGCCATGATG GATACTTTCT CGGCAGGAGC AAGGTGAGAT GACAGGAGAT CCTGCCCCGG
  CACTTCGCCC AATAGCAGCC AGTCCCTTCC CGCTTCAGTG ACAACGTCGA GCACAGCTGC
  GCAAGGAACG CCCGTCGTGG CCAGCCACGA TAGCCGCGCT GCCTCGTCCT GCAGTTCATT
  CAGGGCACCG GACAGGTCGG TCTTGACAAA AAGAACCGGG CGCCCCTGCG CTGACAGCCG
  GAACACGGCG GCATCAGAGC AGCCGATTGT CTGTTGTGCC CAGTCATAGC CGAATAGCCT
  CTCCACCCAA GCGGCCGGAG AACCTGCGTG CAATCCATCT TGTTCAATCA TGCGAAACGA
  TCCTCATCCT GTCTCTTGAT CAGATCTTGA TCCCCTGCGC CATCAGATCC TTGGCGGCAA
  GAAAGCCATC CAGTTTACTT TGCAGGGCTT CCCAACCTTA CCAGAGGGCG CCCCAGCTGG
  CAATTCCGAC GTCTGTGTGG AATTGTGAGC GGATAACAAT TTCACACAGG GCCCTCGGAC
  ACCGAGGAGA ATGTCAAGAG GCGAACACAC AACGTCTTGG AGCGCCAGAG GAGGAACGAG
  CTAAAACGGA GCTTTTTTGC CCTGCGTGAC CAGATCCCGG AGTTGGAAAA CAATGAAAAG
  GCCCCCAAGG TAGTTATCCT TAAAAAAGCC ACAGCATACA TCCTGTCCGT CCAAGCAGAG
  GAGCAAAAGC TCATTTCTGA AGAGGACTTG TTGCGGAAAC GACGAGAACA GTTGAAACAC
  AAACTTGAAC AGCTACGGAA CTCTTGTGCG TAAGGAAAAG TAAGGAAAAC GATTCCTTCT
  AACAGAAATG TCCTGAGCAA TCACCTATGA ACTGTCGACT CGAGCATAGC ATTTTTATCC
  ATAAGATTAG CGGATCTAAC CTTTACAATT GTGAGCGCTC ACAATTATGA TAGATTCAAT
  TGTGAGCGGA TAACAATTTC ACACAGAATT CATTAAAGAG GAGAAAGGTA C

It was sent to me directly from Takara Bio.


Names for effects of sleep deprivation on the brain & body

During extreme sleep deprivation you can briefly fall asleep, this is known as a microsleep. The disorientation that you experienced can be referred to as  Hypogogia.

Hypogogia covers a range of effects including visual and aural hallucinations as well as having thoughts that are experienced as seeming logical during the microsleep but illogical once you're awake.


Are there neuron mediated reactions faster than reflexes?

A reflex as fast as the blink in a neural circuit:

I would consider suppression of outer hair cells in the cochlea to be a reflex; the faster component of this reflex is about the same as the blink reflex, around 100 ms. The hair cells themselves aren't considered neurons, but the pathway that suppresses their motility certainly is.

A much much faster non-neuronal "reflex":

That said, the outer hair cells themselves also dance along quite fast in response to sensory input, even faster than the typical hearing range for humans, faster than 20kHz! In some ways, this is a reflex because you are taking sensory (specifically, auditory) information and turning it into a motor response, but all the "action" is taking place within one cell, and it isn't a neuron.

A more classical reflex that is substantially faster than 100 ms

Reflexes in the periphery can be much faster than 100 ms. The myotatic reflex, or stretch reflex, can be as fast as 30 ms in the knee - this is the reflex that is tested when a physician smacks you on the knee with a hammer (used as a test of spinal and peripheral nerve function, not as a punishment). It's likely there are other stretch reflexes that are faster just because distances to the spinal cord are shorter, but these might be more difficult to test (in this paper they report latencies as fast as 20 ms).

Eyeblink reflexes can also be faster than 100 ms!

For example, see this paper: strong auditory stimuli evoked blinks within about 20ms!

tl;dr: I'd check your source that 100 ms is the fastest reflex! I stuck with mostly human examples here (some of the hair cell work is in other mammals), but you will find even faster reflexes if you look at smaller organisms, such as insects.


What portions of the brain have drastic changes in activation when we "sense" someone is there?

First of all one should tell that one can attribute the activation of certain brain zones with some indepent events only when the activation takes place along the signal input (receptors, sensory pathways towards the cortex and the sensory areas in cortex) or motor action (=output) (along the motox cortex => motor neuron => target organ). Those zones in brain are also termed as primary ones, for there is a clear mapping between the event/action and the activity here.

In case of your "sneak feeling" as you describe in your post, there seems to be more not the sensory input from some unknown type of receptor, but rather a subconscious processing of the complete sensory input that reveals some potential danger and is percepted as a kind of "smell of danger". Since this processing happens in secondary zones and can be well distributed throughout the whole brain, there is no possibility to find a single focus with high activity change here (in my opinion, of course) -- those changes in activity are beyond the measuring/imaging capabilities of modern examination methods.

Possible sensory inputs here might include (but not limited to):

Optical (some shades, moving asyncronously etc).
Acustic (some sneaking sounds, normally disguised by the background sound).
Air move, air stream blocking sense etc (tactile feeling).

So, everything you suggest might apply here.


Identify fuzzy black quarter sized spider with orange on abdomen, in Minnesota

This appears to be some species of jumping spider (family Salticidae).

  [Note that] All jumping spiders have four pairs of eyes, with the anterior median pair being particularly large.

In particular, I believe your specimen is Phidippus audax (Bold Jumper). Specifically, I believe yours is a subadult bryantae variant of this species.

 Source: David Hill 2014

From Wikipedia:

  The average size of adults ranges from roughly 13–20 millimetres (0.51–0.79 in) in length. They are typically black with a pattern of spots and stripes on their abdomen and legs. Often these spots are orange-tinted in juveniles, turning white as the spider matures.

Your specimen shares the orange abdomen with connected black "splotches" that leave an orange triangular dot in the middle. Also, notice your specimen has two grey lines on the posterior cephalothorax as well as black/white striped legs. Finally, 20mm is close to the size of an American quarter (~24 mm).

If you get a good look at the front of your specimen, you'll likely see that the chelicerae are an iridescent/metallic blue or green (a tell tale sign of this species and genus).

 Source: David Hill 2014

 More typical coloration (L) vs. bryantae variant (R). [Source: David Hill 2014]

P. audax tends to prefer relatively open areas to hunt and is commonly found in common in fields and grasslands, as well as on fences, exterior walls, and gardens. Finding one on your car, therefore, would not be so strange, especially given that they can jump 10-50x their own body length (Ruppert et al., 2004).

Phidippus contains some of the larger species of jumping spiders in the family, and it is almost exclusively a North American genus.

Specifically, P. audax is common in southeastern Canada, eastern and central United States and parts of northern Central America, and it has become increasingly common farther West.

Citation:

Ruppert, E.E., Fox, R.S., and Barnes, R.D. (2004). Invertebrate Zoology (7 ed.). Brooks / Cole. pp. 571–584


Mature, viable seeds have to form in most fruits, which involves the maturation of embryonic tissue. That can take a little time, from just a few days in some weed species to months and perhaps longer in some fruits like pineapple.


Really the question how does protein folding work?  But let me answer your questions...

1) Very few proteins have disulfide bonds (usually secreted proteins) or really any covalent bond stabilizing the amino acid chain beyond the bonds that make up the polypeptide itself.  Denaturation is only reversible in relatively few cases in fact.  A few proteins, usually very small ones can be nursed back into a native folded state from an unfolded one, and then only a percentage of the sample will reattain the folded state.

2) Sure.  In fact pressure changes the hydrogen bonded structure of the water and also therefore the thermodynamics of protein structure and has been used to study protein folding. Generally the electomagnetic field does not affect the state of the protein fold.  I cite the fact that many many proteins have been studied via nuclear magnetic resonance, in which the proteins have been inserted into some of the most powerful magnets that can fit into a reasonably sized room.   That is not to say that the protein function might not be affected by such a field.  I'm sure by the time the field is large enough to ionize water or the peptide change you would see something... so you can always push things too the breaking point.

3) Many proteins from thermophilic organisms are more resistant to denaturation and companies actually engineer proteins to be resistant to all sorts of outrageous conditions and still be folded and functional.  Laundry detergent is full of crystallized enzymes that will sit happily in detergent for a long time.  I don't even know if these products have a shelf life.

Overall proteins are vulnerable to denaturation for a good reason- the cell degrades them when it doesn't need their function and can recycle them for their component amino acids. If they were all this robust the cell would starve to death quickly.  If there is a biological role to a protein that is denatured and then refolds itself it is only for extremely rare situations.  Proteins for the most part don't fall apart once they are folded and if they do, they are done.

Some possible exceptions: some antibiotic peptides which fold into pores that kill their targets and the amyloid plaque which takes on a different fold when in the brain which is associated with - but may not cause - Alzheimer's.


Does immunity to CRISPR proteins limit their effectiveness?

Usually not.  the Crispr/Cas proteins can be delivered to the cell as DNA/RNA and the proteins will only exist inside the cell in low numbers.
Even in systems that deliver the protein from the outside in vivo almost always the proteins would be encapsulated in a delivery system to ensure they and any necessary accompanying nucleic acids get into the cell. Getting Crispr/Cas into a cell is difficult to do and they don't just pop in by themselves. They also require guide RNA, which will not easily stay whole in the blood stream and tissues for long.
if you want to just inject a fluid into the blood with unprotected CRISPR/CAS proteins, an immune reaction might stop them.  Not all proteins produce an immune reaction. Sometimes just 2-3 proteins of an entire bacterium produce an immune reaction (antibodies).   But then again its unlikely the proteins would have edited any genomes in any host cells even so.


Is it possible to conduct scientific research without actually getting close to the sample/specimen?

It depends on one's field - whether what you study actually requires first-hand knowledge of the experimental subject and the methods of dealing with or not. Moreover, one could invert the question and ask, whether a field, based solely on the knowledge of the experimental subject, can be considered science?
Theoretical physics/chemistry/etc.
In some sciences, such as physics, there is traditional division into experimentalists and theoreticians - the former are people who actually work in a lab, but who limit themselves to very basic statistical analysis of the phenomena observed. The latter are providing deeper, model-based, analysis of the data and description of the phenomena. Very often their work is not tied to any particular experiment, bordering on very abstract math. Looking at the list of the Nobel prize winners in physics one can easily convince oneself that this work is no less valuable than the experimental work.
Similar division exists in other fields, e.g., one can freely talk about quantum/theoretical/computational chemistry.
Computational biology, bioinformatics, biostatistics, epidemiology, population genetics
Although biology is relatively young science, the times when it was frowned upon by physicists as mere stamp collecting have long been gone: evolutionary theory and epidemiology have been put on a firm mathematical footing, and the explosion of genomic data in the last couple of decades has ushered in the professions of bioinformatician and computational biologist - all complete with designated job descriptions and advanced university programs. Less noticeable, but no else widespread is the observation using modern technology - such as video and sound recording - every conference features a few talks like this, related to swarms of insects, flocks of birds, or behavior of whales (incidentally, whales have been extensively studied in connection to tracing enemy submarines. The analysis of the data is often done very far away from the sea.)

All science is either physics or stamp collecting. - a quote attributed to Ernest Rutherford, but likely of even earlier origin.


Replication refers to DNA replication and division refers to the cell division. Yes it is true that, in E.coli replication can be slower than the division time. This is a well known problem in molecular genetics.

The bacterium copes up with this by having a partially replicated genome during the beginning of the "cell cycle". So there are actually two origins of replication when a new cycle starts. When the replication proceeds you have multiple forks (from the replicated origins). Because of these multiple forks (forks within forks), the replication time speeds up. See the figure below:

 From Fossum et al. 2007

For more details see:

Fossum, Solveig, Elliott Crooke, and Kirsten Skarstad. "Organization of sister origins and replisomes during multifork DNA replication in Escherichia coli." The EMBO journal 26.21 (2007): 4514-4522.

The picture that you have shown is something totally different. As mentioned by Chris, the picture illustrates the Messelson-Stahl experiment to demonstrate the semiconservative nature of DNA replication. Do not confuse that with the above problem. As for the 40min shown from generation-1 to generation-2, in this picture, I feel that it is a misprint.


Elsewhere on SE Biology I have answered a related question regarding enzyme names. Here I will restrict myself to genes, as it seems that this is the main concern of the poster. (In talking about ‘abbreviations’ I think he is referring to what are generally termed gene ‘symbols’.) The answer from @KarlKjer addressed current recommendations regarding gene nomenclature; mine addresses the causes of the current confusion.

Summary

Rules (actually recommendations) did not appear until a late stage in
the development of the field of genetics, when the problem was
already there and there was a need to do something about it.
Historically in animal systems the naming of new genes tended to
relate to mutant phenotypes as this was how they were discovered. The function of the gene that had been mutated was generally unknown.
Sometimes different mutants of the same gene caused different
phenotypes, either because of severity of damage to the protein, use
of animals from a different development stage, or different growth
conditions for bacteria. These mutants appeared to be of different genes, which
were given different names.
Sometimes the same gene was discovered at about the same time by
different workers and given different names in the laboratory while work was in progress and, hence, on publication.
Later it became possible in some cases to identify the products of
genes for which there was no clear mutant phenotype — perhaps just
lethality — and one method of naming was on the basis of the size of the
protein, preceded by the letter ‘p’ (e.g. p63)
The current trend is to try to rename genes according to the function
of their products, where these are known, i.e. to replace the name of a
mutant phenotype by the name of an enzyme or structural protein.
The implementation of such rules or recommendations is imperfect,
depending on the cooperation of authors and editors.

Illustration using some Drosophila genes

I shall use Drosophila melanogaster (the fruit fly) to provide some illustratations of the history of genetic nomenclature, because this was the organism used by Thomas Hunt Morgan (he of the centimorgan) to perform genetic studies after the rediscovery of Mendel’s work in 1900.  His laboratory was responsible for the discovery in 1910 of the first Drosophila mutant, a spontaneous sex-linked mutant that resulted in males having eyes that were white, rather than the normal red. The gene responsible for this mutant was named white, initiating the custom of naming genes after their mutant phenotype. (Drosophila gene names became italicized by convention.) What else could they have done? Not only was the protein product of this gene unknown, the whole idea of genes encoding proteins did not yet exist. The abbreviation (symbol) for this gene was merely w. Clearly, nobody anticipated that another 17,000 genes would follow, or suggested that a committee on gene nomenclature should be set up.

It is interesting to note that the product of the white gene was not identified until almost 90 years later. In 1999 it was established that this was a member of the ABC transporter family, responsible for bringing  into cells the guanine and tryptophan  needed to make the red pigment so characteristic of the eye of the wild-type Drosophila. The human version of white was identified roughly contemporaneously by sequence homology, and although it was initially referred to as hW (human homologue of white) is now named according to its gene product: ATP-binding cassette sub-family G member 1 (ABCG1). Its function in humans — who only have red eyes in flash photographs — is in lipid transport.

The era of of molecular genetics in the late twentieth century brought an avalanche of new genes, many not associated with a particular phenotype. The culture — accepted by scientific journals — was that if you discovered a new gene you had the right to name it as you pleased. A generation of young scientists were pleased to chose names that reflected twentieth century, rather than classical, culture. Flip through the names of Drosophila genes (try the autocomplete here) and you will find alien, bazooka, cactus, Dorothy, ether a go-go all the way to zucchini. Nor was it only the Drosophila geneticists that were responsible for this. The hedgehog segmentation gene, discovered in Drosophila, has three human homologues. One of these was named ‘sonic hedgehog’, which I am informed is the protagonist of a children’s video game. O tempora, o mores!

A couple of final points will be made to illustrate the problems of nomenclatue of Drosophila genes. Several other mutations of the white gene have been observed which have different phenotypes (e.g. result in different eye colour). This is because they involve insertions into the gene rather than its complete deletion. This also illustrates one historic difficulty that could result in several names for the same gene. The other point is that many of the genes identified by genome sequencing, at least initially, were associated with no mutant phenotype and had no known function, and were so named simply be an accession number (CG1234 etc.). As functions emerged they would be renamed. And an example of the nomenclature situation can be seen in the NCBI entry for Drosophila gene TfIIS (RNA polymerase II elongation factor):

  Also known as: BG:DS00929.12; br52; CG3710; Dmel\CG3710; DmS-II; DmSII; l(2)35cF; l(2)35Cf; l(2)br52; l35Cf; RnpSII; TFIIS; TFIISA; TFS-II


Dogs bark at familiar person in Santa costume. Why? Don't dogs trust smell over vision?

The dog was probably freaked out by the weird costume.  Humans do it all the time (I've been seeing Halloween decorations for sale since early August, which is terrifying) but we generally comprehend what's going on.  Dogs may not fully understand the idea of a costume, much as a human infant might be scared by masks or beards (or the sudden removal thereof).

Anyway, this 1997 article titled Canine fears and phobias; a regime for treatment without recourse to drugs is kind of a fun read and has some interesting tidbits about, go figure, canine fears and phobias.  One thing it discusses is the importance of the primary associations brought on by sight, smell, and hearing.

  However with a fear of hot air balloons the dog will hear the propane burner and see the balloon but a primary (coming from the balloon), olfactory cue will be missing.

Missing out on that is enough to freak 'em out.  This research article from the 1950s is a little more exact/thorough and has what you want.  It's worth reading in more detail if this topic interests you, but the part that answers you is here (emphasis added):

  Some at least of the test objects could not have been discriminated by smell, as with the bronze deer, or the mechanical turtle, and in the course of the work it was frequently clear that visual cues were affective before olfactory ones could have been. Vision also can dominate olfaction: fear of a modelled human head was observed although the model was completely wet with dog urine.*

Likely what happened was the dog saw a weird/scary/new person and, were upset that their vision and smell didn't match up, and continued being freaked out.

(*The urine experiment comes from this article out of 1944 Germany, in what is now known as Ethology, in case you feel like reading German.)


Spinosaurs (like Spinosaurus) are currently only known from 112-97 million years ago, although isolated teeth push the origin possibly back to ~150 Mya. At least now, there isn't any definite spinosaur material younger than 97 Mya.

So spinosaurs were already extinct when the rest of the non-bird dinosaurs went extinct at the end of the Cretaceous, whether by meteor impact, volcanism, a combination, or something else completely.


How hard it is to determine a 3d structure of a protein?

Experimental protein structure determination is hard: the most common method is X-ray crystallography, which can be done in a few months if you are lucky and can take years if you're not. The problem with X-ray crystallography is that you need good protein crystals, and in most cases, proteins don't crystallize very well, so it takes a lot of time (and a lot of purified protein) to get the right crystal. (In the comments section Cody added some good links with more in-depth abut X-ray crystallography for structure determination relating to ATP synthase).

The cost is mainly based on the materials & manpower you need for this, and you need to test a lot of different solutions to crystallize your protein in, which aren't very cheap. If you don't have access to specialised equipment for making the crystals (mostly pipetting robots) or the measurement (X-ray beamline), this is going to be super expensive.

Crystallography requires protein crystals, which are sometimes too troublesome to obtain. Other methods that do not require crystals, such as NMR and cryoEM, are even more difficult to perform though less luck dependent. These techniques rely on very expensive equipment and often cannot resolve the structure as precisely as protein crystallography. So unless you can find one of the few people who have experience with these methods, you'll run into a lot of additional problems.

There is also computational structure prediction, which only needs a powerful computer. However, unless your protein is very similar to one with a known structure it will probably not work reliably. As mentioned in the comments there are web server's for the established methods and progress is constantly made on new(er) algorithms, so depending on your needs it's definitely worth a shot to try computational structure prediction.


Blood volume is not a dimensionless number - it's a volume. Historically we used to measure this in patients or volunteers by giving a large carbohydrate molecule like a starch that is not digestible or harmful to the body. Just like every other body fluid compartment volume (i.e. plasma, interstitial fluid, intracellular and extracellular) that we have, blood volume is estimated by intravenously injecting a known concentration of a particular compound. Once that compound equilibrates you take a blood sample and measure the compound's concentration again.

Initial Concentration * Initial Volume = Final Concentration * Final Volume

When you inject a known volume of a known concentration that only fills the "blood" component, and then you measure a final concentration - you can then solve for the "Final Volume" for "blood volume".


I don't wash my hands and never get sick. Any theories?

You may very well be strengthening your immune system, but there are microorganisms that you don't want to get, which can have longer term health consequences. For example, there seems to be a significant increase in developing MS if you've ever had the Epstein-Barr virus. But this is just one case. You also don't want Salmonella, tape worms, etc.

So there may be a price to pay for a stronger immune system: namely higher probability of exposing yourself to the more dangerous things out there.


I think it would be hard to delineate what secretions are specifically because of phagocytosis, because in that sort of environment you have multiple types of cells secreting things, and multiple signals through such pathways as toll-like receptors (TLRs). So, I looked at papers involving activated professional phagocytes such as macrophages and neutrophils. The secretome of the activated cells follows a somewhat typical pattern for innate immune cells: IL-1ß, TNF family, interferons, IL-6, IL-8, and a host of other chemokines and cytokines (1, 2, 3). Mast cells of course secrete things such as histamine in response to Fc-receptor stimulation and TLR signaling.

Non-professional phagocytes like epithelial cells lack receptors to make phagocytosis efficient, but I'm far less certain about the body of data on non-professional phagocytosis. We know that activated epithelium and endothelium secrete inflammatory signals to attract immune cells, for example, like IP-10 which attracts CXCR3-expressing cells.


Furry Bug that swarms only certain plant

As indicated in @KarlKjer 's comment, this insect is a Pseudococcidae, or commonly known as Mealybugs. The exact species is difficult to find due to picture quality.

Mealybugs are insects in the family Pseudococcidae, unarmored scale insects found in moist, warm climates. Many species are considered pests as they feed on plant juices of greenhouse plants, house plants and subtropical trees and also act as a vector for several plant diseases.
Mealybugs occur in all parts of the world. Most occur naturally only in warmer parts, and get introduced into greenhouses and other buildings in cooler countries. It is unlikely that any live in the Arctic or Antarctic, except perhaps in buildings.

Considering that Mealybugs are found basically anywhere on Earth, it's not a surprise to have found them in Israel.


Can plants break down cellulose for energy?

Plants do not produce extra cellulase to break down cellulose for an energy boost when they are grown in dark conditions (that I know of). But remember, cell walls are the structures maintaining turgor pressure in the cells, so breaking them down would be very costly to plant survival. A couple notes: plant cell walls have more components than just cellulose, and they ARE dynamic. In dark-grown conditions, plants elongate (etiolation) during which time, enzymes (expansions) break down cell wall bonds to allow the cells to elongate the stems of the plants. Elongation is an evolutionary advantage to find light when things get shady.

To read more about what the cell wall is made of, and the function it provides to the cell, try watching the Khan Acadamy video about cell walls. Light signaling is an entire field in Plant Biology (example). Read more, if you are interested in how immobile plants handle shading from other plants or periods of darkness. Plants do break down proteins for reuse! Read more about plant vacuoles if you're interested in how they recycle and break down some molecules and proteins when needed (related to your question's parallel to animal cells; although, not cellulose breakdown to replace photosynthetic sugar output).


This can happen when DNA separates after melting and then reanneals.

You likely will not see this in chromosomal DNA in the cell, but I would assume it can happen to RNA molecules sometimes as they are single stranded and can self-anneal.

Mostly though, we think about this issue when performing PCR or DNA/RNA hybridization assays. Shorter pieces of DNA will be more likely to bind and anneal incorrectly, especially if the DNA is rapidly cooled after it has been melted.

Rapid cooling does not give the DNA time to "test" the different combinations of complementarity and sometimes can get stuck in a place where there is very little complementarity.

You also need to remember that while A-T G-C hydrogen bonding is favored, bases are able hydrogen bond to other bases, it just makes the double stranded molecule less stable.


Why does plucking nose hair cause tears in the eyes?

Also, tears are an intrinsic pain response and considering the dermal-derivative nature of hair, there are loose nerve endings ensnaring the follicular area, so the sensory neurons detect pain and tears are a physical manifestation of the pain, cuing the body to avoid that stimulus again.


Do Class A biosolids count as organic fertiliser?

Definition of "organic" in Science

In science (esp. in chemistry), organic matter loosely refers to matter that eventually make up living beings are are remains of living beings. Typically organic matter consists of long chains of carbon surrounded by hydrogen atoms and a few oxygens and nitrogens (and eventually other things such as sulfur and phosophorus).

Can we eat something that is not organic?

Unlike plants, we (all animals and fungi) are heterotrophs (feed on organic matter only). As a consequence, there is no such thing one could call food that would not be organic.

The (mis)use of the term "organic" in popular culture

In the popular culture organic is a term that tries to refer to certain type of food that are grown under certain conditions and treated a certain way. However, there is really no good definition of organic in the popular culture and there exists no objective definition that would satisfy someone that wishes to categorize food into what they like to call "organic food" and "not organic food". Similarly there is no good objective definition of GMO either.

Some organization may make up definitions of "GMO" or "organic food" but those definitions rely on a long list of products rather than to an actual definition.

I just want to attract the attention of the naive reader that I am not saying that the term organic as used in the popular culture is healthy/not healthy or good/bad. Arguments concerning whether it is ethical to buy organic food goes both ways and it is not the job of a science website to discuss questions of ethics.

Are GMO safe to eat?

You are not asking this question here. But in case you wonder you might want to have a look at the Skeptics.SE post: Is Genetically Modified food safe to consume?


Can Two Opposite Running Action Potential Cross Each Other without Annihilation in One Axon

Combining the lecture notes on the interchannel and channel  electric potential leads to a description of the propagation of the action potential $V$. Specifically, substituting in $I_{\text{ion}}=I_{\text{ext}}$ of equation (6) of cable theory by equation (1) of Hodgkin-Huxley model gives the full propagation equation. A linearization of the Hodgkin-Huxley model leads to a system of linear partial differential equations. I will write out the full formulation and the linear approximation later. That allows complete superposition of action potential. The original non-linear system of partial differential equations under a set of functions/parameterizations at least close to the linear version should permit two opposing wave to cross each other though with interference. So it is not true that all parameterizations of the Hodgkin-Huxley model prohibit two-wave-crossing.
It would of course be intriguing to investigate the existence of a particular form/parameterization where the model does extinguish two opposing waves with its initial condition being two pulses close to a dirac delta function at each end of the axon.
Here is a paper M. Argentina, P. Coullet and V. Krinsky, Head-on Collisions of Waves in an Excitable FitzHugh-Nagumo System: a Transition from Wave Annihilation to Classical Wave Behavior a special case of the Hodgkin-Huxley model. Just as I expected, the waves do not always annihilate each other, but rather may cross, annihilate or even coalesce or even coalesce then re-emit, all depending on the particular values of the parameters of the model. Another paper Oleg Aslanidi, O. A. Mornev, Can Colliding Nerve Pulses Be Reflected? on the numerical simulation of a full-blown Hodgkin-Huxley model reporting crossing of colliding waves. This paper Follman et al, Dynamics of Signal Propagation and Collision in Axons reports under their particular set of parameterization of Hodgkin-Huxley model, two colliding waves annihilate. This paper by Alfredo Gonzalez-Perez et al demonstrates Penetration of Action Potentials During Collision in the Median
and Lateral Giant Axons of Invertebrates based on the soliton theory of nervous signal propation as described in On soliton propagation in biomembranes and nerves by Thomas Heimburg and Andrew D. Jackson.
The wikipedia page on autowave has some interesting information including references for propagation and collision of nonlinear waves in excitable media.


Could cyanobacteria thrive with very high CO2 concentrations and almost no oxygen to start with?

I like this exobacteria theory question because they implement a strategy for answers that may go against or for the idea of out of space terraforming. Simply providing detail won't be enough in this case. Cyanobacteria are not very durable in Venus atmosphere. The temperature of Venus is of much higher average and they will be feeding of the atmospheric pollution as well causing an oxidative affect on the cell when too much co2 gives off oxides. But more importantly hydrogen buildup in the protein folds could cause inhibitory stress (prevents binary fission). So no I would not use Cyanobacteria as a space project. But please go against me if I'm false.


Confusion on polarity and hydrophobicity of Proline, Tyrosine and Cysteine?

TL/DR: these are borderline, complicated cases. There is no broad consensus on whether cysteine and tyrosine should be considered hydrophobic or polar. Proline is clearly nonpolar though.

The reason for the confusion is that are there several ways to define and measure polarity and hydrophobicity for amino acids. First, the polarity and hydrophobicity of the free amino acid is very different from that of the amino acid side chain in the context of a peptide (protein). I assume you are interested in the latter.

Polarity is rather difficult to define for amino acids. The dipole moment is the usual measure of polarity, but this depends on the molecule's geometry, and consequently is only well-defined for small molecules that cannot "wiggle" around, such as water. Larger amino acids side chains can wiggle quite a bit, and their dipole moment is difficult to define. Instead, polarity is usually given by rules of thumb like "hydroxy groups are polar" and "aromatic rings are nonpolar. But then there are borderline cases like tyrosine that has both an aromatic ring and a hydroxy group.

Hydrophobicity is related to polarity, but it is an experimentally measured quantity, usually determined by how an amino acid partitions between water and nonpolar solvents, or by observing how it orients in folded proteins (towards or against the water solvent). More detailed information is found here. But the results of such experiments don't always agree, and so amino acids which are borderline hydrophobic/hydrophilic can be difficult to classify. For example, for two amino acids X and Y, we might find that X dissolves better in water than Y, so X appears more hydrophilic in this sense; but at the same time, X could also partition better into a lipid bilayer, so in this sense X appears more hydrophobic than Y. In such cases, the various scales of hydrophobicity will differ.

For these reasons, there is disagreement on whether some amino acids are polar/hydrophobic. With this in mind, here's my two cents on the amino acids you mention:

Proline is a bit special in that it does not have an -NH3 group; the amine nitrogen binds to the side chain -- it is more of a "loop" than a chain -- and the peptide bond is different. But this "side loop" clearly has no polar group, and I think there is good agreement that proline should be considered nonpolar. The Khan Academy page is probably mistaken on this one. Proline is intermediate in hydrophobicity.

Tyrosine: As mentioned, polarity of the tyrosine side chain is unclear since it is quite large and has both polar and nonpolar groups. Tyrosine is somewhat hydrophobic, but among the amino acids, it places itself near the middle on most hydrophobicity scales. So tyrosine is a borderline case, which explains why different sources disagree.

Cysteine is special in the context of proteins, since cysteine residues often pair up via disulfide bonds, and this changes its properties. By itself, the -SH group is polar (although less so than an -OH group) so the cysteine side chain is somewhat polar. It is intermediate in hydrophobicity as measured by solvent partitioning. Cysteine was considered hydrophobic based on the observation that cysteine is often found in the interior of proteins, away from the water solvent; but this is largely due to its ability to form disulfide bonds.


Examples of real biological applications of the Keller-Segel system

This looks like a good starting place: Painter, K. J. “Mathematical Models for Chemotaxis and Their Applications in Self-Organisation Phenomena,” June 22, 2018. https://arxiv.org/abs/1806.08627v2 (published in Journal of Theoretical Biology, 2019). Lists examples from Dictyostelium (of course), bacterial aggregation, development, physiology and disease, ecology, social science.

In this review, I evaluate the use of PKS [Patlak-Keller-Segel] models in describing chemotaxis (and other taxes), particularly focussing on examples of pattern formation/self-organisation. I do not review the numerous excellent studies
that primarily concentrate on their mathematical analysis: a number of reviews already cover these aspects in depth [...] Next, the fundamental modelling that led to (1) is reviewed and an overview given regarding its patterning behaviour. I then proceed field-by-field, beginning with its motivations in microbiology and sweeping across areas including developmental biology, immunology, cancer, ecology and the social sciences. For each case, the historical justification for chemotaxis is described and models are discussed; a compendium
that contains many of these models is provided in the Appendix. Finally, I demonstrate how PKS models can continue to penetrate new areas, via a novel application to explain clique formation in research.


Soil contamination or soil pollution is caused by the presence of xenobiotic (human-made) chemicals or other alteration in the natural soil environment. It is typically caused by industrial activity, agricultural chemicals, or improper disposal of waste. The most common chemicals involved are petroleum hydrocarbons, polynuclear aromatic hydrocarbons (such as naphthalene and benzo(a)pyrene), solvents, pesticides, lead, and other heavy metals. Contamination is correlated with the degree of industrialization and intensity of chemical usage.

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

  The acute health effects of hydrocarbon mixtures are generally associated with exposure concentrations at thousands of ppm. However, the exposure concentration and exposure duration leading to the onset of acute health effects varies between individual hydrocarbons, and this may influence the effects of exposure to mixtures.Health effects associated with a single exposure to hydrocarbons are asphyxiation, narcosis (ie depression of the central nervous system; anaesthesia), cardiac arrest and aspiration. Of these, the first two are probably the most significant in the offshore context.

http://www.hse.gov.uk/offshore/notices/sn_04_04.htm

  In relation to the assessment of vapour risk,petroleum hydrocarbons and chlorinated hydrocarbons differ in their potential forvapour intrusion (VI) risks, primarily because petroleum hydrocarbons (PHCs) readily
  biodegrade in the subsurface when sufficient oxygen is available(USEPA 2011,2012a). Hence while a number of aspects of this guidance are general and can beapplied to a range of volatile compounds, the guidance is intended to specificallyaddress PVI and should not be applied to sites contaminated with other compounds
  including chlorinated hydrocarbons and landfill gas.

http://clu-in.org/download/issues/vi/CRCCARETechreport23-PetroleumhydrocarbonvapourintrusionassessmentAustralianguidance2.pdf

  Organic compounds can be a major pollution problem in groundwater. Their presence in water can create a hazard to public health and the environment. This page will focus on the BTEX's which makes up one of the main groups of soluble organic compounds that find their way into our soil and groundwater. One of the most common sources for BTEX-contamination of soil and groundwater are spills involving the release of petroleum products such as gasoline, diesel fuel and lubricating and heating oil from leaking oil tanks. Because of their polarity and very soluble characteristics, the organic chemicals (BTEX's) of petroleum products will be able to enter the soil and groundwater systems and cause serious pollution problems.

http://www.webapps.cee.vt.edu/ewr/environmental/teach/gwprimer/btex/btex.html

  Petroleum vapours at percentage concentrations are flammable, potentially explosive
  and acutely toxic; lower explosive limits (LEL) for many volatile hydrocarbons are in the
  low percentage range. Petroleum vapours are denser than air. Some components of
  petroleum vapour are also chronically toxic at trace concentrations and as such are also
  considered under the heading VOCs [volatile organic compounds ].

http://www.epa.nsw.gov.au/resources/clm/120932GroundGas.pdf

This document contains site investigation details which describes how to find traces of compounds in soil and water.
.


Term for trait that is advantageous to a population only as long as it is rare

Frequency-dependent selection is the term you are looking for, I believe. Positive frequency-dependent selection encompasses traits that become more advantageous as they become more common. Negative frequency-dependent selection encompasses traits that become more advantageous as they become rarer.


Are the number of base pairs in a given chromosome same between different individuals?

Welcome to Biology.SE.

  if I take an X-chromosome from two random humans would I count exactly 155,270,560 base pairs in both cases

No, you would probably not find the exact same number of base pairs because mutations do no only change one nucleotide to another (what we call a substitution) but sometimes add or delete few (or sometimes many) nucleotides.

note, btw that you don't need to take two different individuals, you can just consider the two X chromosomes of a female (or any other pair of chromsom in any gender) and find this difference in the length of chromosomes.

  what's the range in length variation?

Good question (+1)!

Telomere issue

Before I start, I want to make clear that I consider the length of those chromosomes at the moment of conception. Chromosomes will vary in length during the lifetime due to telomere reduction. I will not consider this in the following calculations. Also, some mutations directly introduce (or delete) a large number of nucleotides (transposable elements for example), I am not considering those mutations here, assuming they are rare in comparison to to single insertions and single deletions (this assumption might not hold!). So please really take the following with a grain of salt.

Let's make some messy calculations

In classical theoretical population genetics, we tend to consider mostly substitutions. But I can maybe try to make some extrapolation out of this work if you allow me to make some strong assumptions, use poor estimates of actual true values and using some non-rigorous mathematics! This is going to be ugly and not extremely trustful $\ddot \smile $.

Not explaining why this is true (it is a result coming from Coalescent Theory), the expected number of pairwise differences between two neutral sequences for a diploid population is $E[\pi] = 4\cdot N\cdot \mu$ (quite an impressively simple result), where $N$ is the population size (assuming panmictic population) and $\mu$ is the mutation rate for the whole sequence. Assuming a constant per site mutation rate of $\mu_s = 10^{-9}$. Knowing the length of the sequence of interest (chromosom X) $L ≈ 1.55 \cdot 10^8 $, the mutation rate for the whole sequence is $\mu = L\cdot \mu_s = 0.155$. Let's consider a population size of $N = 5 \cdot 10^7$ (the equations assume a panmictic population so I just took some value that felt more or less reasonable to me much smaller than the actual worldwide population size). Therefore the total number of substitutions should be $E[\pi] = 4 \cdot 5 \cdot 10^7 \cdot 0.155 ≈ 10^7$.

Now, let's assume that only a fraction of $\frac{1}{100}$ of the mutations bring variation in the number of nucleotides, we might want consider the value $\frac{1}{100} \cdot 10^7 = 10^3$. And because a mutation that deletes a nucleotide from a long sequence will rather diminish the number of variant in sequence length that increasing it, let's say that will divide this number by 10!... so I'd say that two typical X chromosome would differ in length by about 100 nucleotides.

I am sure that with some work one can come up with more rigorous calculations and a more accurate expectation. Intuitively, the result of 100 nucleotides doesn't sound totally crazy (it is not 1 nor 10^6 at least).

Also, one could probably use available sequence data to estimate this value.


The muscular fibers (or more exactly the actin and myosin filaments) are contracted towards each other. This makes them "move to the middle" and you build up a force on both sides of the muscle. See this image (from the Wikipedia), which illustrates this process:

There is also an animated picture available, which illustrates this process even better (from here):

The process of the contraction applies a equal force to both endpoints of the muscle.


What is the relationship between complexity and organization in biology?

Here's food for thought. Entropy is always considered to flow naturally in a direction of order, to disorder. That is, the higher entropy a system has, the greater degree of disorder it has, and the less amount of work it can perform.

Now, look at a cell. It is a biological system of organic molecules that are able to organise themselves in a way that outweighs the forces of entropy. To "fight" the natural tendency of the universe that moves toward a state of disorder requires a highly complex system. And, in the process of going against entropically favorable mechanisms, a cell is also able to produce its own energy (stored as potential energy, or ATP if you will).

I guess you could say, a more complex system is able to organise itself in a greater number of ways for the purpose (and I use this word very loosely, as nothing really has a purpose) of yielding entropic energy to do work.


Why are microtubules absent in and around the nucleus?

tl;dr Cells are 3D and the cytoskeleton does not exist within the nucleus.
There are several things you have to be aware of when looking at such pictures. Remember, you are looking at a 3D object which is not homogeneous and uniform in depth.
Shape of a plated HeLa cells
You are looking at HeLa cells. When plated like in your case, they adhere to the plate and make a generally thin, 2D-ish shape with lamellipodia (the extruded parts that look like they are grasping the plate on the sides of each cell). The nucleus is the most prominent vertically bulging part of the cell - the nucleus takes up most of the depth of the cell and there is little space around it. You have to appreciate the vertical dimension of the cell around the nucleus especially. The shape is a little like an egg cooked sunny side up; the yolk makes a bulge and the egg white is thinner around the yolk and there is little space for large filaments like microtubules. Remember, cytoskeletal filaments are so in size: small (actin) filaments < intermediate filaments < microtubules. This is exactly why you see more actin, a little less intermediate filaments, and even fewer microtubules exactly on top or below the nucleus in these 2D plated cells. Also, please remember that these cells are not representative of most cells.
The nucleus is a separate compartment
The nucleus is also a separate compartment, within which the actin and microtubule cytoskeleton system do not exist. The nucleus performs its own structure-keeping in the form of the nuclear lamina, which is composed of protein meshes that sit on the inner membrane of the nucleus.
You are not seeing the small actin filaments inside the nucleus, only around it. The microtubules are too large to see above and below the nucleus in most cases, since they are much larger filaments. In some cases though, you would see microtubules in HeLa cells above and below the nucleus.
See picture below: microtubule stain shown in green.

Other images for a more wholesome appreciation of the cytoskeleton.
Here follow a few micrographs of HeLa cells.
In green, actin.
In red, intermediate filaments stained with vimentin:

And now here you can see a microtubule stain in HeLa cells, in pink. Notice that some microtubules do actually make it around and across the nucleus.


The stinger that got stuck in your partner's skin isn't completely black. Its coloration shifts from dark brown near the abdomen to black to dark brown again at the tip of the stinger.

This identifies the stinger as one belonging to Vespula vulgaris, the common wasp as the stinger of the other most common stinging insect in Scotland (Apis mellifera or European honey bee) is honey brown to brown.

Once in a while a wasp can happen to get its stinger torn of when it's flicked away during its sting. Obviously it dies afterwards as also part of its intestines are torn.

Pictures of both stingers can be found below.


Let us start with difference between humans and crocodiles. There are lot of differences but the one which matters in current discussion is thermophysiology.

Unlike humans, crocodiles are cold blooded animals (more specifically ectotherms). These animals needs to get heat from environmental sources to maintain their body temperature. As contrast to humans who can get heat from internal metabolism. That is the precise reason crocodiles are seen always not moving and basking in sun light when it is cold (while go to shade or water if it is hot). Read this for more elaborate strategies they use. If you want scientific reference, you can check this, this or this.

On your exercise point, there are few reports which suggest exercise can enhances aerobic capacity in young crocodiles. In this study they actually put crocodiles on treadmill and checked affect on their respiration. This report suggest  crocodile uses 3 different kinds of muscle mechanisms for lung ventilation. These three act differently in different conditions (means one acts during rest while other during high metabolism). However I couldn't find any information regarding atrophy.

  how can crocodiles remain so fit if they don't do any exercise? What distinguishes animals that need to exercise to be strong from animals that don't?

Short answer: Their body metabolism.

Their body metabolism is different from human's. Although doing exercise  might help in their aerobic capacity as mentioned in reference above.


Why is there a difference in the rotation of the tail fin in fish compared to marine mammals?

While fish tend to move from side to side (lateral undulation) for which a vertical tail makes sense, the land ancestors of marine mammals had their limbs under them and so their spines were already adapted to up and down movement (dorsoventral undulation). When these animals moved to marine environments, they continued up and down movement in their swimming, for which a horizontal tail makes sense.

(The wikipedia article on fins gives some more detail, and links to this webpage on Berkeley.edu. A paper by Thewissen et al. suggests that for cetaceans, dorsoventral undulation as a swimming strategy came first, and the horizontal tail evolved later.

More detail:

In a third example beyond fishes and marine mammals, the icthyosaurs and other aquatic reptiles developed vertical tails, even though like marine mammals they evolved from four-footed land animals. This may be because the legs/spines/gaits of land reptiles differ from those of land mammals, so that the earliest icthyosaurs swam with lateral undulation, as reflected in their spinal modifications.

This blog post by Brian Switek gives a really superb run-down on the issue, with figures and citations. I'll quote this part which deals with the dorsoventral undulation theory:

  ...mammals and their relatives were carrying their legs underneath their bodies and not out to the sides since the late Permian, and so the motion of their spine adapted to move in an up-and-down motion rather than side-to-side like many living reptiles and amphibians. Thus Pakicetus[the pre-cetacean land mammal] would not have evolved a tail for side-to-side motion like icthyosaurs or sharks because they would have had to entirely change the way their spinal column was set up first.

Switek goes on to to talk about exceptions in some marine mammals:

  At this point some of you might raise the point that living pinnipeds like seals and sea lions move in a side-to-side motion underwater. That may be true on a superficial level, but pinnipeds primarily use their modified limbs (hindlimbs in seals and forelimbs in sea lions) to move through the water; they aren’t relying on propulsion from a large fluke or caudal fin providing most of the propulsion with the front fins/limbs providing lift and allowing for change in direction. This diversity of strategies in living marine mammals suggests differing situations encountered by differing ancestors with their own suites of characteristics, but in the case of whales it seems that their ancestors were best fitted to move by undulating their spinal column and using their limbs to provide some extra propulsion/direction.


Where exactly is 'Colloid' with regards to synthesis of thyroid hormones?

Colloid is found in thyroid follicles and is composed of the protein from which thyroid hormones are made.

This link below states: "Follicles are filled with colloid, a proteinaceous depot of thyroid hormone precursor."

That precursor is called thyroglobulin.

The image below shows micrographs of the thyroid.

In the image, the colloid is surrounded by thyroid epithelial cells, which collectively form a follicle. The lower mag on the left shows many follicles filled with colloid.  The image on the right shows one follicle. The white areas inside the follicle near the epithelial cells show uptake of colloid by the epithelial cells, which are activity synthesizing thyroid hormone.

http://arbl.cvmbs.colostate.edu/hbooks/pathphys/endocrine/thyroid/anatomy.html


Why is there a mass limit on biological powered flight?

One of the physical limits to biological flight is muscle physiology.

Muscle force output is proportional to muscle physiological cross sectional area (PCSA) multiplied by its specific tension (Gans, 1982):

$$F = \text{PCSA} \times \text{Specific Tension}$$

PCSA is basically just the cross-sectional area of a muscle adjusted for its architecture. Pennate muscles have higher PCSA than parallel fibered muscles, because more fibers are packed into the area (at the cost of shorter functional distances). Specific tension is the force output per unit area. For a single species, specific tension is essentially constant.

So the way to make more force is to make more PCSA. But muscles don't scale only in area, they scale in volume as well. Increased volume increases mass as a cubic power, but muscle area only scales as a square power. So any increase in area that requires a volume increase (which is inevitable), will quickly outstrip any gains in force output.

Note that this doesn't mean that very large flying vertebrates were not possible: the largest pterosaurs (e.g., Quetzalcoatlus) had ~15 m wingspan and perhaps weighed 200 kg and the largest birds (e.g., Argentavis) had ~7 m wingspan with a mass over 50 kg. Both, however, were likely gliders.

Gans C. 1982. Fiber architecture and muscle function. Exerc Sport Sci Rev 10:160–207.


What is the name of this tree with yellow flowers?

Looks like this one: https://en.wikipedia.org/wiki/Peltophorum_pterocarpum
Peltophorum pterocarpum or the Copperpod


No. PCR (and quantitative PCR, or qPCR) rely on primers. They will amplify DNA flanked by primer regions, and this 'multiplied' DNA will be detected (and quantified).

PCR can be used to detect DNA. Reverse transcription followed by PCR (RT-PCR) can be used to indirectly detect RNA. Neither method is used to detect protein abundance, or post-translational protein modifications such as phosphorylation. This is because the modifications are not inherently encoded* in the nucleic acid sequence. They occur only on the protein level. Also, the abundance of a transcript tells you very little about how much protein will actually be produced from it, and how long this protein will remain in your biological system. A single mRNA can result in two very differently-modified proteins, and PCR would not be able to distinguish between an mRNA producing one kind or another. Also, phosphorylation is often a temporary modification, it's good to remember that.

*unless you have transcript variants (that produce protein isoforms) which omit or gain sequences that are modifiable, in the environment of a specific biological system.


How does the peptidoglycan layer of a bacterial cell wall help prevent osmotic lysis?

Peptidoglycan is formed by the linkage of molecules of NAM ( N-acetylmuramic acid) and NAG (N-acetylglucosamine) into a polysaccharide structure.  Many of these structures are then formed into a lattice by crossbridges of polypeptides.  In gram + bacterial cell walls many layers of this lattice are stacked up forming a rigid structure, that is external to the plasma membrane, and provides more resistance to osmotic lysis than the plasma membrane alone posesses.

Penicillin interferes with the final linking of the peptide crossbridges which results in a weaker cell wall that will make it more likely that the cell will undergo osmotic lysis.

Gram - bacterial cell walls are quite different than gram + cell walls.  They do contain peptidoglycan but the peptidoglycan layer is thinner - only one, or very few, layers of peptidoglycan with some structural differences also.  Therefore, gram - bacterial cell walls are weaker than gram + bacterial cell walls.

"Microbiology, an introduction" Tortora, Funke and Case 11th EDition pp 84-86


Why don't breast enlargements leave any marks of surgery on breasts?

All cuts that go through the dermis (the full thickness of skin) will leave a scar, no matter what (and no matter what anyone tells you). The visibility of scar tissue has a lot to do with how a person heals, how much stress is put on the incision as it's healing, where the scar is, if it crosses the natural direction of skin (called Langer's lines) or goes along the lines.

Plastic surgeons have many years of training and experience in cosmetic skin surgery, and know how to minimize scar formation by their more fastidious closure methods and wound care, as well as hiding scars in ceases and along Langer's lines. But even the best plastic surgeons cannot prevent scars, only minimize them. If you still don't believe breast augmentation doesn't leave scars, you can look at this page (NSFW).