Does the nature of nervous impulses give us a finite number of things we can perceive? This is a subject that is very disturbing to me and one that I've been obsessing over for years. I warn you now that this is probably not the sort of thing you get asked on this website and I'm not even sure if I'm explaining it very well but please bear with me.

I have, or at least used to have, a great passion for art and have always been a very creative person. But years ago I began obsessing over the idea there are only a finite number of possible images that we can perceive. And therefore everything I have ever created or will ever create is part of a predetermined, limited set of possibilities.

The amount of knowledge I have about how perception works is that when light hits a photoreceptor in the eye it fires electricity into its connecting nerve cell, this triggers the nerve cell to zap the next one and so on until it reaches the brain. The brain has a memory of where each chain of nerves is connected to and so it identifies that otherwise indistinguishable zap as coming from a particular photoreceptor in the eye. That each chain of nerve cells simply transmits it is on or off and nothing else. I worried that meant our perception works exactly like am LED screen, meaning that when light shines on the grid of photoreceptors, the image that gets sent to the brain is made of dots of exactly one solid colour and the only reason we don't notice it because the brain smooths the edges. This would mean that, if eyesight works like a digital camera there is a finite limit of things that we can possibly see because there is a finite number of images you can possibly create with a digital camera.
I even found an article on the Internet that claim that's exactly how it works, they even have a diagram:

Eventually I found a way around it when it turned out that the eye is constantly making microscopic movements even when holding still.

But what about hearing? I know we have sensors in the form of hairs that trigger a nervous impulse to the brain when they are stimulated. But as I understand it, each one can only send that on/off binary signal when they are triggered by a very specific level of sound. What happens if there is a sound that is in between two hairs? Do you simply not here it? Is the same true for all the sensors we have?

I know that the brain processes a lot of what is sent. I know that there are things outside our range of perception such as ultrasonic and UV light. And I know we all have our personal reactions and even perceptions. But none of that matters to me.

What I want to know is, can our senses cover a continuous spectrum? Or, is everything we perceive a number of discrete and finite possibilities made up of digital, pixelated, quantised information? Can we only perceive image A and image B with nothing in between, or can we perceive image A.012744 and A.064212454 And A.24545157845?

I know we have sensors in the form of hairs that trigger a nervous
  impulse to the brain when they are stimulated. But as I understand it,
  each one can only send that on/off binary signal when they are
  triggered by a very specific level of sound.

Your overall question borders on philosophy and the biology of consciousness which is hardly understood at all. However, your picture of sensory input is a huge oversimplification. That's not really your fault, it's the sort of thing you are likely to pick up from pop science descriptions, which in turn are faulty because this is not a dead field where everything is understood to a T. Even the question of which parts of perception "are" digital and which "are" analog is still under investigation. However it makes your question hard to answer because it's sort of ill-posed since is assumes a purely digital model.

To address one oversimplification, our perceptions of the outside world are not necessarily binary on off bits. It is hypothesized that some neurons signal by changing the rate at which they fire. Is the rate continuously variable? It's not clear, but it certainly provides a much larger range of encodings than 1 and 0.

  Can we only perceive image A and image B with nothing in between, or
  can we perceive image A.012744 and A.064212454 And A.24545157845?

I don't know how this meshes with your statement that 'And I know we all have our personal reactions and even perceptions'. If you've ever looked into color blindness then you already know that some of your fellow humans can't distinguish between A.012744 and A.064212454, even if you can. It's not that they can't see them, they just can't tell that they are different.


Why does the pH decrease, when adding pancreatin to different types of milk (cow milk, soy milk etc.)? I'm experimentally observing how pancreatin affects the pH in different types of milk.
Why does the milk's pH decrease when I add an enzyme solution to different types of milk (e.g., cow milk, soy milk etc.)?
I am not sure how to explain this reaction.

Thank you for your help.

the pancreatic fluid contains lipase which breaks down the fat in the milk in to fatty acids and glycerol. The fatty acids produce lower and create a more acidic pH.


Did Plant Cells Evolve from Animal, Protist, or Fungal Cells? I know protists and animals preceded plants but I am unaware of when fungi arose in relation to plants. At the moment, I cannot find a resource stating how plants evolved from existing kingdoms, or whether they evolved independently from prokaryotes. Thanks for the help, sorry if this is common knowledge.

Plants were almost always considered a separate group from fungi and animals.

As per the latest classification both animals and plants are included in the clade Opisthokonta: animals and related unicellular organisms (holozoa) form a sister clade with holomycota (contains fungi and Cristidiscoidea).

Plants (archaeplastida), aveolates and rhizaria are now grouped under Diaphoretickes (previously they were grouped under Bikonta).

To cut short the plant and animal lineages merge only at the level of the last eukaryotic common ancestor. This means that plants are as unrelated to fungi as they are to animals.

Protista is no longer considered a proper clade. It used to be a group where all unclassified unicellular eukaryotes were dumped. Now these organisms have been reclassified; some are closer to animals (for e.g. Amoeba), some are closer to plants (e.g. Plasmodium) whereas some are part of a group that is distantly related to both plants and animals (for e.g. Euglena).

Have a look at this WikiSpecies site for a detailed classification (latest and historical). It also cites proper references.


Amino acid characteristics that determine their chemical properties? What chemical aspect of amino acids results in their having different properties such that the chemical and physical properties of polypeptides vary with both amino acid content and amino acid order?

Sounds seriously like your homework, so it'd be better if you researched. However as a starting point amino acids can be polar and non-polar. These properties cause varying forces of attraction between amino acids and their surrounding environment. The location changes the way they can interact. Ask if you are unsure about something :)


Evolution experiment for kids? What would be a good plant to show the process of evolution to a small kid? Obviously it's a long term experiment, and preferably a fruit or a veg that is edible (like tomato?), and what characteristic would be (size, colour) good to select for?

This is for an animal, not a plant. But, when I was in school, the Peppered moth was used as an example of rapid evolution from the 19th century. Its white coat made it very noticeable against soot-stained surfaces so it had a rapid selection pressure to become black. If you can organise a trip with your kid to a natural history museum, you might be able to find some specimens.


Protein structures given in PDB and SNP's There are millions of proteins given in PDB, the sequence for which we can download in FASTA format. There are also hundreds of SNP's given in NCBI dbSNP. My question is whether the proteins in PDB incorporate the SNP's into their structure? If not, is there a way to visualize protein structure using any tool after a SNP on the protein? I know that tools like SIFT exist but they only say whether or not a SNP is harmful or not. They don't comment on the structure of the protein in anyway.

Swiss PDB Viewer allows you to mutate residues in an existing structure and explore the effects.

I'm pretty sure that UCSF Chimera does too.


What is the difference between these two depictions of chromosome? I understand that this is a single chromatid, but would this be considered a chromosome? Also before mitosis, the chromosomes appear as single chromatids but during interphase they replicate to form sister chromatids which are attached by a centromere and are also collectively known as a chromosome.
I do not understand the difference between the two of them. Are they both to be termed chromosomes?

Here is the thing, chromosome refers to a lot of different things ( however, all are coiled up DNA).

Let me explain step by step.
You have DNA, it has a diameter of 2nm, it is coiled with histone proteins and make 10-11nm fiber. This is what we refer to as the chromatin fiber(Beads on a string). At this point we are in interphase where too much coiling is not required because a lot of transcription, replication going on. At the S phase of the interphase, DNA replication takes place and sister chromatids are formed or do they? The answer is yes and no. The thing is even though DNA has replicated and coiled upto certain extent, we dont call the replicated dna as sister chromatids because we only consider them to be sister chromatids when we can clearly see them as separated threads connected at centromere during the M Phase.
So, to put it in simple words, you have the sister chromatids formed (during the S phase) long before you are actually calling them as sister chromatids, you just wait for them to condense further and when you can finally see them as distinguishable threads you call them as sister chromatids.

Now, your real question can be answered. You have posted two chromosomes, one green and the other is red, red has two chromatids connected at centromere. Lets start with the red chromosome. The red one is the metaphase chromosome. Try to remember cell cycle. You have your DNA replicated by the S phase of interphase, then comes G2 and then M Phase starts with prophase, at this point your chromatin fiber gradually starts getting condensed and by the end of prophase, your 10nm coiled DNA (Chromatin fiber) ends up coiled to 700nm fiber but remember, you have two 10nm fibers connected at centromere after the S phase but they were so thin that you could not distinguish the two threads separately, now you can because they coiled in a very organized manner and now you have two 700nm fibers attached at the centromere, this is the maximum condensation achieved and as this final condensed version is observed at the metaphase it is named metaphase chromosome.

So, the red one is definitely a chromosome. What about the green one? That too is a chromosome. the green one is formed at the next step of cell cycle that is anaphase. Here the two sister chromatids split at the centromere and move towards the opposite poles of the cell as  new chromosome. but wait, haven't I called them sister chromatids throughout the answer and suddenly calling them chromosomes? Yes, the previously called sister chromatids are called as  individual chromosomes the moment they are separated from each other at anaphase.

So in summary, the thread like structure that you see in interphase are coiled DNA(Not called chromosomes), chromosomes are also coiled dna but the difference is that these are way more coiled. The red one is metaphase chromosome (1400nm) with two sister chromatids(700+700=1400). The green one is also chromosome but these are actually sister chromatids that got separated at anaphase(only 700nm), you can call them as daughter chromosomes

I hope this helps


How much does a typical biologist know about signal processing, machine learning, and (theoretical) computer science? How much does a typical biologist know about signal processing, machine learning, and (theoretical) computer science?

Coming from a neuroscience background where knowing about algorithms and computer science is a must, it seems to me that in biology there is much less cross disciplinary work. Though, yes, there are bioinformatics (but you only do sequence alignment and clustering?).

Anyway, given a typical PhD student in biology, how much does he/she need to know about programming, signal processing, etc?

I don't know what a "typical" biologist is, but I'd guess they don't know much about computers, because the population in general is computer illiterate. In my department, we do have a lab that does a lot of computational work on proteins. And of course bioinformatics relies on computers.

I can see where programming would come in handy for an ecologist, and maybe hardware and electronics too. Lets say you want to track animals in the woods. Traditionally, you'd give them a radio collar, then you'd have to triangulate their position in the woods, and at the end of the day all you'd have is location data. You could use something like a Raspberry Pi or Arduino to create a device that has GPS, a camera, and cell phone antenna, which could record much more information about the animal's location and activity and send it back you without as much effort.

In our modern computerized age, knowing some programming is always a plus, no matter what field you're in. Finding ways to apply that skill aren't always easy. I know both Java and C++, but I've really only written a few programs that I've used in research, 1 to calculate number of possible peptides given a size and some amino acids that won't change, and one to calculate how much DNA to use in ligation reactions.


Are there medical treatments that were so effective they were never subjected to a randomized control trial? I'm thinking of things like antibiotics for meningitis or tuberculosis, or thiamine for Wernicke-Korsakoff syndrome. In those cases the magnitude of the treatment effect might have been so great that it would have been unethical to assign subjects to a placebo group. However, I couldn't find any sources to attest that randomized control trials were never done in relation to those treatments.

I'm referring to treatments trialled in a time and place in which randomized control trials were an option.

In recent years, clinical trials are all necessary. You have to have the randomised control To make sure it isn't a placebo effect. If and only if the drug seems to be super effective will they cut the randomised control short and give the real drug to everyone.

Sadly, while it may seem unethical, there was a cancer treatment that two cousins got into. The normal treatment guaranteed death, while the new drug actually had people practically bouncing off their death beds. One got the placebo - in this case normal treatment since it's unethical to not at least give standard care - and the other got the drug. The drug worked so well, the doctors tried to push to cut the trial short but they wouldn't and the one on the normal treatment died.

This drug was PLX4032.

blogspot uproar

clinical trial information

NYTimes article

So to my knowledge about clinical trials, no trial has been able to skip that stage. It's actually Called Phase III testing of the drug, followed by Phase IV which is administration to the public. It can, however, be shortened if it is promising enough.


For how long would a flu-contaminated parcel be an effective disease vector? A parcel has been delivered and contaminated by a person who has the flu.

For how long would the parcel be an effective disease vector?

How long should I wait before handling the parcel to avoid contracting the virus?

If you use gloves, or don't touch your face and just wash your hands after opening, you don't have to wait at all.  If you don't use gloves or want to pick your nose, rub your eyes, or fiddle with your beard while opening the package, wait 24 hours if the package is nonporous, and 2 hours if it is not. Generally, whether contaminated or not, don't lick, eat, inhale, or rub your eyes with the package :)

Influenza and similar respiratory viruses are transmitted by large droplets, aerosols, and fomites. Your package is a fomite, an object that can be contaminated and transmit disease. There is some debate about what mode of transmission is most significant for influenza, but fomites definitely do transmit influenza and similar viruses. In a study of homes and daycare centers with children who had an active influenza infection, 59% of home objects that were tested were positive for influenza. It's reasonably likely that your package was, at least at some point, contaminated.

@LDiago's answer is useful here, but deserves some clarification. The UK National Health Services information cited in that answer comes from this seminal study. I'm not entirely happy with the wording on the NHS website, though. Virus survives on nonporous surfaces for 24-48 hours. Virus is transferred from nonporous surfaces to hands in detectable amounts for 24 hours. If your package is paper, the relevant test is transfer from cloth or paper. Virus survives for 8-12 hours, and is measurably transferred to hands after 15 minutes to 2 hours. In any case, virus transferred to hands from a fomite survives for only 5 minutes.

Infection from fomites, however, requires virus to be transferred from the fomite to (typically) the hand, and then from the hand to respiratory tract epithelium. Inoculation of nasal passageways is sufficient for infection in laboratory conditions. Conjunctival and oral inoculation may also play a role. You can read more about this in Cecil Medicine Ch. 372 and Murray Medical Microbiology Ch 59.


white blood cells and cancer cells transport through lymphatic vessels It is a well-known fact that both of these cells can reach the lymphatic vessels from interstitial space. How does it do so physically? Are there any mathematical models describing this process? It seems like there are endothelial cells along the lymphatic vessels that act like valves, so I would assume that these "valves" open, the cancer cells/WBCs would fit through to reach the lumen?

This question is also a reference request. I am looking for papers that describes the process of intravasation of WBCs and cancer cells into the lymphatic capillaries? Mathematical models are preferable but this is such a niche topic that probably there are no mathematical models.

The "valves" are basically one way valves that just prevent backflow of interstitial fluid from the lymph into the interstitial space, so they do not specifically affect the flux of WBCs, cancer cells, etc. into the lymph vessels. In terms of a mathematical model of flux into the lymph vessels, you could use Poiseuille's law to determine the flow rate of interstitial fluid through the "valves", then multiply by the concentration of WBCs, etc. in the interstitial fluid to get the flux of the given cells into the lymph vessels. Of course, that is just one possible model for one parameter (cell flux).


Online resource for downloading gene variant data? I have a long list of gene variations. For example, Here are 4 of them:

CBL Q249E

TERT H412Y

SF3B1 R625H

EGFR L747_T751delinsP

The first term identifies the gene, the second identifies the variation.

I am a data scientist with no background in biology or medicine. I am looking for an online resource where I could download synonyms, descriptive data, and other relevant info for all the gene variants.

I have seen two sites where data is offered for some gene variants, but not for others. For example, the EGFR L747_T751delinsP variant is well documented at this and this site.

While CBL Q249E is documented at the ckb.jax site but not the reactome site. Other variants are documented at reactome but not ckb.jax, etc.

Plus, there appears to be no easily downloadable file containing this data. Before I go scraping what I need off of a hodgepodge of websites, I wanted to check with you smart people to see if there is a user-freindly resource out there that has this data in a downloadable format.

Seems your variants are all possibly harmful mutations to human genes, in that case ClinVar can be quite useful, it returns hits to all your variants except L747_T751delinsP. I have never used the ClinVar API so I'm afraid I can't vouch for how easy to use that is.

When ClinVar doesn't have the variant (or info about it) you need you could search EBI to see if other sites have information for this variant, when queried with L747_T751delinsP EBI actually shows us that it has been entered into Reactome twice. (welcome to the mess that is sequence annotation!).

This might be outside of your scope but if you have an interesting variant that you cannot find information on you could try to find the most similar (known) variant using BLAST.


How does a cell identify itself? In embryological development, undifferentiated cells developed into specific types.  As far as I understand, a key differentiating factor is the regulation of gene expression via transcription factors.

However, if all cells have identical genomes and, therefore, identical transcription factors, what is the source of difference in their morphogenesis? Does it rely on some element of randomness in external factors?

This has been studied this in Drosophila, and a lot of development hinges on where the cell is in the body.  An initial asymmetry of mRNA in the pre-fertilized ovum leads to the establishment of the anterior-posterior axis (which end is the head, which is the tail)  So cells are told what to develop into based on what mRNA signals they receive which depends on where they are along that axis.

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


How semi-synthetic cell with artificial DNA works I know that by now this is old new but I heard that a cell that used a synthetic pair of nucleotides, called X and Y, have been made. My question was, how did the cell understand the X and Y nucleotides during translation and how was it even represented in mRNA? It must have been represented differently, possibly using X and Y nucleotides only. That's the only way I can think of that causes the cell to make 172 amino acids instead of the usual 20. By the way I read this in the Discover magazine, January issue.

The altered E Coli still only made use of the regular 20 amino acids (presumably).

Looking at the original citation, Malyshev et al didn't characterize the RNA in their altered E Coli at all. All they did was add free X and Y to the E Coli's growth medium and add a gene to the E Coli that expressed an algal nucleotide triphosphate transporter. Malyshev et al then demonstrated that replication (copying of the DNA) proceeds normally and in such a way as to preserve the X and Y content.

So no information as to whether any of the products downstream from the DNA (ie mRNA, proteins, etc) were affected by their modifications.


Do cuttlefish know how to mimic animals since the moment they are born or do they learn by observing? I can't seem to find information anywhere else so I hope somebody can help me out.

So, as the question states, I saw a cuttlefish mimicking a hermit crab the other day and I was wondering if cuttlefish carry information of what they can mimic as spiders carry information of how to make a web (innate behaviour) or if they learn how to mimic by observing other animals.

I haven't been able to find any definitive research/answers, but, based on the usage of their mimicry (camouflage and sexual), and some of its features (alteration of the surface texture of their skin, electric camouflage, development+change through lifetime), I'd hypothesise that it's most likely a mixture of the two. They likely have a large innate capacity to use the form of mimicry young cephalopods do, which is further developed socially/as a learned behaviour, which subsequently causes the change in the nature of their mimicry.

Cuttlefish texture change (Primary research article)

Transient sexual mimicry (Summary article (Nature))

Research has shown that cuttlefish mimicry develops and changes as they grow; it has also been shown to differ based on the location of the creature. There is also evidence of cephalopods learning socially, so it does indicate that their behaviour is at least partially learned. (Source + additional references- reed.edu ->Visual Mimicry in Cephalopods -> Ontogeny)


Why are bugs attracted to light bulbs but not flames? Just now, a housefly was bugging me a lot and I wanted to get rid of it. My mother suggested me to turn off the lightbulb and off it went. However a small flame was burning in my room. Why didn't the housefly get attracted to the flame (although it was a luminous flame)?

My first guess is because of the high temperature a flame produces. This Wikipedia article states that:

  A 300 watt tubular halogen bulb operated at full power quickly reaches a temperature of about 540 °C (1,004 °F)

And a charcoal fire can produce temperatures between 750–1,200 °C (1382-2192 °F). Source.

I've seen small bugs getting attracted to large halogen lights in sports complexes. Although these two temperature ranges are a sizable difference apart, 540 °C doesn't seem cool at all. Is it really due to temperature, or is there some other reason?

It has nothing to do with temperature, but with the color of the light. Insects are especially attracted to lights with short wavelenghts, especially Ultraviolet (UV) light. Yellow and red light attract far less insects. (Rich & Longcore 2006). PDF

White light, like the one emitted by an average light bulb, consists of a broad spectrum, that includes UV. Halogen lights also emit UV. Flames on the other hand emit mostly red and yellow light.

Unless the flames burn at a very high temperature, then the flames turn blue. To illustrate this, my parents used to have a candlelight on gas they used during camping. This light burnt at a very high temperature, and hence the flame had a bluish color. And it did attract insects, especially moths.


Bacterial cell lysis - what solution to use? I am trying to determine how quickly detergents act on bacterial cells (cell lysis). I would like to compare some detergents at difference concentrations for bacteriolytic activity. I don’t care about all metabolites inside the cells (proteins, DNA, etc…). Many publications suggest that often more complicated solutions are used. My first thought was to use a simple prepared detergent in PBS or saline for lysing the cells. Do I need a complex solution to lyse the cells?
Could someone please give me a suggestion? Thanks in advance.

What exactly is the purpose of lysing the cells? The "complicated" solutions, as you say, include a bunch of ingredients. The detergent is largely present to dissolve cell membranes (which are lipid-based) and allow for extraction of proteins or other biochemicals from within the cell (and organelles in eukaryotes). There are also two types of detergents: ionic and anionic. Both detergent types will dissolve membranes, but ionic detergents tend to be harsher of the two by strongly disrupting protein structures.

If protein biochemistry is important, then the next most important ingredients will be specific inhibitors of proteases: enzymes which degrade proteins. There are many of these, but some examples include PMSF, EDTA, aprotinin, etc.

Sometimes it is necessary to buffer the pH of lysis solution to monitor protein complexes, or keep a protein natured, or keep DNA in an optimal pH range. General solutions for lysis buffers include Tris-EDTA (TE), PBS, etc. This choice comes down to whether you want a buffer, and in which pH range you wish to keep your lysis solution. Common buffers like TE and PBS are made up for a pH range of between 7-8. There are other buffers that are used for low pH ranges (pH 4-6), but are usually less common.

Lastly, there are ways to lyse cells without using any kind of lysis buffer. One method is to use sonication, which uses directed pulses of high-frequency sound to lyse cells by mechanically shearing them. Another method is to repeatedly freeze-thaw cells from -80°C to 4°C (usually 3 times is sufficient). Lysis in this manner is accomplished by repeated formation of ice crystals which cut open cells, releasing their contents.

If you have a more specific question, one of us can guide you further, but this provides a general overview of what is involved with cell lysis buffers.


Why human endometrium doesn't stay constant? Is there any explanation or evolutionary advantage to the endometrium constantly cycling between the proliferative and menstrual cycle? Wouldn't it be more advantageous if it kept always fully thickened? I imagine it is less energetically expensive than to be always producing and losing all those cells, blood vessels, etc.

One hypothesis is to protect the uterus and oviducts from sperm-borne pathogens.

Also Beverly Strassmann has proposed that the energy savings of not having to continuously maintain the uterine lining more than offsets energy cost of having to rebuild the lining in the next fertility cycle, even in species such as humans where much of the lining is lost through bleeding (overt menstruation) rather than reabsorbed (covert menstruation).


Are triglycerides fat? I have a quick question: Are triglycerides essentially what we call "fats"?
I've tried reading up on it but there seems to be some conflicting information.
Thank you.

Fats include free fatty acids and their compounds with glycerol: mono-, di- and triglycerides.

In a cooking context, fats refer to solid fats, and oils to fats that are liquid at room temperature. Most of them contain triglycerides.

Fats belong to a broader group--lipids--, which are substances that are usually not soluble in water and usually soluble in certain organic solvents, such as ether or acetone. Besides fats, lipids include sterols (cholesterol, plant sterols), waxes, lipid-soluble vitamins (A, D, E, K) and steroid hormones (aldosterone, corticosterone, etc).

Examples of complex lipids are phospholipids, glycolipids and lipoproteins.

Fats and lipids are often used as synonyms. However, you usually say dietary fats and blood lipids.

http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/lipids.htm
http://biology.about.com/od/molecularbiology/ss/lipids.htm


How would cloning affect conservation of rare species? Many species are at risk of extinction, and cloning could be seen as a relatively quick method to produce large numbers of members of the species to aid in conservation efforts, especially if the species involved has low fecundity (such as the giant panda).

However, cloning results in the reduction of genetic diversity, which may lead to significant issues due to inbreeding and susceptibility to diseases. This can most clearly be observed in the Gros Michel banana cultivar, which was nearly wiped out by Panama disease due to the cloned banana cultivar not having any resistance to the disease.

What are the main positive and negative aspects of cloning when applied to conservation of rare species?

(This question is based in part on this question, which was closed for having not done any research, but has an interesting premise that I wish to see answered on this site.)

Cloning become an important method for conservation genetics. However, it is not a magical solution and doesn't solve all of the the problems. There are two key considerations with conservation: short term issues which are causing the immediate threat such as poaching, habitat destruction etc. and long term issues of genetic variation. Genetic variation is critical to the long term survival of a species because low genetic variation results in inbreeding depression (reduced ability to survive and reproduce resulting from higher expression frequencies of deleterious mutations) and reduced potential for adaptation. The rate of adaptation is determined by the strength of selection and the volume of genetic variation; without genetic variation there can be no adaptive evolution. Therefore, genetic variation is key to the long term success of a species.

Where cloning can come in is it can be used to increase the gene pool, sometimes quite substantially. Consider the meta-population of a species, this could be allowed to include all of the wild sub-populations and all captive or managed (semi-captive) populations. For example, there are ~3900 wild tigers in the world, and ~5000 in captivity. Among all of those, only a subset contribute offspring to the next generation of wild animals, reducing the effective population size, and increase rates of inbreeding and genetic drift. For example, often very few males fertilise the females of a population with strong effects on the effective population size. What cloning could be used for (to various levels, depending on the specifics of the method) is to allow other individuals to contribute. For example, by cloning the members of a wild population that were unable to secure mates during a reproductive season (there is often high variance in mating success which reduces effective population), conservation managers can artificially re-inflate the effective population size to more closely resemble the census population size. In other cases, conservation managers may chose to clone particularly viable/fertile individuals that are approaching old age or nearing death, and are therefore at risk of being lost from the population. Conservation programs could use cloning of (semi-)captive individuals and introducing clones from (semi-)captive populations in to wild populations allowing genetic variation to be drawn from the gene pool of (semi-)captives in to the wild populations. Increasing the variance in the gene pool will increase the adaptive potential of the wild population. Another option is to clone wild animals in threatened areas (e.g. where populations are in decline as a result of poaching) and to put the clones in to safer areas such as national parks, or even zoos, to preserve genetic variation while conservation managers try to bring the other issues under control. Effectively this would act a bit like a seed bank.

However, there are some issues to consider, and this is a non-exhaustive overview. What if there was a good reason for some individuals not mating? The action of selection, which causes adaptation, is to induce variance in reproductive success as a result of the genes an individual carries: in principle selection reduces genetic variation and allows the "better" variants to prosper. So if we clone a wild individual that produced no offspring in the reproductive season we may just be maintaining genes in the population that selection would otherwise be removing. In other words, cloning efforts could be counter-productive to the long-term success of the species and make conservation more difficult. What if we reintroduce bad genetic variance to the wild population? Captive populations have adapted to some degree to the environment that they are in, this may have selected genes out of those populations that are more beneficial in the wild. For an extreme example, dogs are descended from wolves and have adapted to an enormously different environment, so it would probably be very counter-productive to start cloning chihuahuas and introducing them to wild wolf populations as a conservation strategy to get genetic variation from captive "wolf" populations (but maybe the chihuahuas would be a good food source at least). Can clones be effectively, and efficiently, reared and introduced to wild populations? It will be extremely hard to actually get to the point where clones can be successfully introduced to wild populations. Resources (including money), are extremely limited in conservation, so there may be better ways to use those resources. Are populations under remaining threat from short term issues such as poaching and habitat loss? If there is continued extrinsic threat to the wild population then there is not much use in cloning, because clones will also be threatened by the same issues. Many places are still under serious threat from poaching. Adding some clones would be like trying to stop a ship from sinking and using a tiny bucket to bail out the water; you need to plug the hole first or use a really big bucket (can cloning be a big enough bucket?).

Bonus: You could read here about the issues faced in the Isle Royale system of wolves and moose, where wolves are on the verge of extinction, and the impacts it will have on the ecolsystem.


What does "genetic correlations" mean as opposed to just correlations? I'm reading the paper "Large-scale GWAS reveals insights into the genetic architecture of same-sex sexual behavior". In Fig. 4 shows "Genetic correlations of same-sex sexual behavior with various preselected traits". This sentence confuses me. I understand that you could do a standard statistical analysis to find correlations between same-sex sexual behavior and various traits. What makes the way they are doing the correlations "genetic"?

(Note: This may be more of a statistics question than a bio question. Feel free to move it to a more relevant SE site.)

It is simply a correlation where one of the two variables considered is the genetic state at a given locus. In a GWAS, one loops through all loci and systematically performs a correlation analysis between the genetic states at this locus and the phenotypic trait of interest.

In the example of sentence you cite

  Genetic correlations of same-sex sexual behavior with various preselected traits

They looped through each polymorphic locus in their data set and at each locus they performed a correlation analysis between the two variables "genetic states at a this locus" and "same-sex sexual behavior" (whichever way this second variable is recorded).

A study might also be interested in more than one phenotypes. In such case, different phenotypic variables can either be considered separately or can be included in the same analysis through linear models. It is for example not so unusual to include one of the variable as a covariatiate in an ANCOVA type of design.


Are there any pairs of animal species that regularly prey on other? I don't mean cannibalism within a single species - I mean, are they are any pairs of species A and B such that members of species A regularly prey on members of species B, and also members of species B regularly prey on members of species A? I'm considering adults preying on other adults of the other species, not on individuals early in their life cycle.

Caiman and Anacondas - though each hunts the other at a stage of development when the hunter is larger.1 2
Occasionally this occurs with Orcas and Sharks.3
Some species of shark3
Spiders and mantids4
Alligators and catfish (catfish prey on infant alligators)
Many species of predatory fish
Some species of constrictor and venomous snake.
Some frogs and Epomis circumscriptus / Epomis dejeani5
Some amphipods6
In Antiquity, hominids and lions7 8
Big cats preying on eachother, among other large predators:

Carnivores eat a variety of vertebrates: e.g. desert coyotes eat … carnivores (roadrunners, reptiles, and mammals)… Carnivorous mammals often overlap substantially in diet (30). Many “readily prey on other carnivores” (125), e.g. tigers prey on bears (black, brown, and sloth bears), dogs, wolves, lynx, and badgers (125): leopards prey on lions, cheetahs, wild dogs, and spotted hyenas (also raptors, crocodiles, and pythons; …
Leopards are mutual predators with lions, spotted hyenas, tigers, large raptorial birds, crocodiles, and pythons…

The Ecology and Evolution of Intraguild Predation: Potential Competitors That Eat Each Other


Family tree for edible plants? I am looking for a family tree for plants, particularly veg / herbs / fruit.

Something similar to:

If it could be slightly less technical than all the Latin names too :). The aim is to easily find out what plants are related such as Cabbage, Broccoli, sprouts, Cauliflower (all Brassicaceae). Currently having to look them all up on Wikipedia which is quite painful.

Another example, but a plant version.

Basically just search "thing you want" and "phylogeny" and you'll find a million results on Google.  For you, I might recommend the Botanist in the Kitchen blog, which has a whole page on the subject and has assembled this phylogeny, including many, many others.  It's pretty impressive!


What is the extent of the effect of Tris on E. coli? I was a fool and dissolved my antibiotic (Kanamycin) into Tris Buffer rather than H₂O. The Kanamycin still seems to be active but a fellow labmate mentioned that Tris messes around with the membrane permeability of cells. I was curious to what extent this actually influences experiments.

Tris(hydroxymethyl)aminomethane buffer modification of Escherichia coli outer membrane permeability.

The cited article describes effects of Tris on the outer membrane of E. coli. Like all Gram negatives E. coli has an inner (or cytoplasmic) membrane which is a typical phospholipid bilayer membrane containing many membrane proteins including transporters and, of course, an electron transport chain. Surrounding this there is a layer of peptidoglycan, and then the outer layer of the cell envelope is the outer membrane, which is a special (highly atypical) bilayer structure containing phospholipid and lipopolysaccharide as well as a number of proteins including the porins. The space between the two membranes is the periplasm, or periplasmic space which contains a number of small secreted proteins.

The outer membrane is susceptible to disruption by a number of treatments including EDTA treatment. For example, many cell lysis procedures for E. coli use EDTA to disrupt the outer membrane sufficiently to allow lysozyme to gain access to the peptidoglycan.

Cells with destabilised outer membranes could display increased fragility, but in general I would imagine that this would not normally cause any specific problems: obviously this would depend upon exactly what your experiments are.

Finally it is worth noting that the concentration of Tris that you will be adding with your kanamycin must be pretty low. Even if you have used 0.1 M Tris you are presumably using a 1000x stock, so the final concentration of Tris will only be 0.1 mM. The work in the cited paper looked at cells resuspended directly in 0.1 M Tris. I don't think that you need to worry about this at all.


Are codons that map to the same amino acids interchangeable? From wikipedia, in the section on the RNA codon table, I see a mapping between codons and amino acids. There, Valine is related to GUU, GUA, GUG, GUC.

Does it mean in the same context that these four codons are interchangeable? Could one replace GUU with GUG?

I think given that you're just getting started with genetics, you can say that the codons are interchangeable. This is generally true, though not technically correct. Here are a few reasons for why this is the case, though there's probably more:

Specific organisms use specific codons with different frequencies. This is usually related to the tRNA abundance in the cell. Using a codon for which there is relatively less tRNA available would be expected to lead to a decreased protein synthesis rate.
Using different codons can affect mRNA secondary structure, which could affect expression.
Some codons, especially stop codons, can influence translation contextually through a process called recoding. This can include frame-shifting, read-throughs, cleavage or, perhaps most famously, coding for the amino acid selenocysteine and much more. See here.
Different codons can also influence translation contextually through pausing. This affects the rate of protein synthesis as well as its folding. See here.
Changing codons can affect regulatory sequences such as miRNA binding sites. Though these are usually present in the UTRs, they can also occur in the CDS.


Is the size of the genome across species roughly the same? Chromosome number differs across species.

Is the amount of DNA comparable between organisms, just being split into smaller chunks in those species with more chromosomes, or do species have different genome sizes? If so, does the genome size correlate roughly with the complexity of the species?

Chart of C-values (the mass of DNA in a single haploid cell); there is no logical order to the groups:

[source]

Base pairs in haploid genome (some examples):

Escherichia coli (bacterium): ~4.5 million
Caenorhabditis elegans (nematode worm): ~100 million
Homo sapiens (we all know what these are): ~3 billion
Pinus taeda (coniferous tree): ~22 billion
Prorocentrum micans (single-celled algae): ~245 billion

From these data we can conclude:

Different species do not have the same genome size.
Genome size is not correlated with complexity. Organismal complexity can be hard to define but, qualitatively, I think we can all agree that a human is more complex than a single-celled alga. And yet, humans have a genome that is 80 times smaller. This is known as the C-value paradox. Note, however, that this paradox has been resolved after it was found that the genomes of most eukaryotes contain a large proportion of non-coding and repetitive DNA.

Further reading:

The C-value paradox, junk DNA and ENCODE by Eddy SR

Eukaryotic Genome Complexity by Pray L


The difference between the beta-sheets and the quaternary structure of proteins My biochemistry book says that beta-pleated sheets is a form of secondary structure of proteins, and it is formed between two or more polypeptide chains.

I wonder why the sentence in bold doesn't belong to the quaternary structure instead?!

Quarternary structure is between separate protein chains or proteins themselves. Beta sheets are a form of secondary structure which is within a single polypeptide.

Sure, some of the structures in quarternary complexes will be between “two or more peptide chains”, but the stipulation that these not be part of the same polypeptide chain would be necessary.


What kind of fish is this white blue-stained fish? This fish has been spotted at the Great Barrier Reef near Cairns (Queensland).
I put a big effort to find it via Google but never could encounter anything similar.

I have also made an attempt to find this fish here with no luck.

I don't know whether this helps, but that looks like a parrot fish.  I had a look online and also didn't find anything with that distinctive pattern. The closest I could find was Scarus ghobban (common names include blue-barred and blue-trim parrotfish), which is highly variable but the blue edges on the fins seem constant.

According to the sources linked above this fish can be seen in areas with sandy bottoms, so that seems consistent with your photograph.

Reference pictures:


Tiny white very hard cell bug! Please help to identify! I found these bugs walking on the floor/ wall and on my laptop.  And unfortunately I think they could be in my bed, too, since I bring my laptop to bed sometimes.

I live in a big city in the Netherlands without pets. My house has humidity issues.

I have noticed that the bugs are very tough to exterminate; meaning that when trying to squeeze them it really needs a lot of effort for their size. Their size is about 1 - 2 mm and their color is whitish.

Please note that my lightbulb is having a yellow color.so it makes it look darker than normal. It's more white than looks in the picture

This is a pic of it walking on my screen...

Definitely an arachnid and mite (subclass Acari), and very likely a member of the order Parasitiformes, of which there are more than 100,000 species!!

The body plan is not all too different from a tick (order Ixodida), but the movement of your specimen in the video doesn't seem to match that of typical tick. As such, I next began examining species in the related order Mesostigmata.

Unfortunately, according to here, a clear detailed shot is needed to ID this specimen confidently:

  In most cases identification of Mesostigmata to family or lower can be accomplished only if the specimen is an adult female. The easiest way to determine the stage and sex of your specimen is to look at the intercoxal region.  Adult females have a genital opening that is almost invariably in the intercoxal region (species of Metagynella are exceptions) and covered by a sclerotized shield which may be truncate posteriorly or continue onto the ventral region.

However....

Mites just always seem to be associated with birds in urban homes, so I thought I'd do some google sleuthing....and voilà! I've found a near and reasonable match!

Specifically, your specimen looks quite similar to mites in the genus Ornithonyssus of the parasitic family Macronyssidae -- these are bird mites (or possibly rat mites). According to here,

  The tropical rat mite, Ornithonyssus bacoti, is one of the most common house invading species. The tropical fowl mite, Ornithonyssus bursa, and northern fowl mite, Ornithonyssus sylviarum, are also frequently encountered in homes. The latter two species are found principally on domestic or wild birds. The house mouse mite, Liponyssoides sanguineus, may also be found in structures with house mouse infestations. The tropical rat mite is a parasite on rats. Although none of these species are truly parasitic on humans, they bite people readily, often producing dermatitis and itching.

As for knowing the specific species, citybugs.tamu.edu suggests:

  Distinguishing between different species of Ornithonyssus mites to determine whether birds or rodents are the likely source is difficult and requires special expertise.

You can read more about Ornithonyssus bacoti, Ornithonyssus bursa, and Ornithonyssus sylviarum on Wikipedia, and you can see videos of these mites crawling on people here and here.

According to here, Ornithonyssus bacoti can be found as far North as Iceland.

 See below for images:

 Rat mite (Ornithonyssus bacoti). <1 mm;  © Erling Ólafsson; Source: www.ni.is

 Ornithonyssus spp.; Copyright 2014 Tom Murray; Source: bugguide.net

Note: I do not know this group of organisms well, so my answer serves as an (educated) guess to get you on the path toward proper identification...


Twist in the DNA double-helix DNA, has a deoxyribose sugar — phosphate backbone with the purine and pyrimidine bases, adenine, cytosine, thymine, and guanine connected to the deoxyribose sugar. (The base–sugar molecules are nucleosides, and those with phosphate, nucleotides.) In the double helix structure of DNA the two strands are twisted and connected by hydrogen bonds between the bases.

How is this "twist" created in the cell, and why is it necessary?

First, your description is accurate. The only pedantic critique I would make is that the technical term for nucleotides in DNA is deoxyribonucleotide.

Second, I don't want to say that non-helical DNA never occurs since the structure of any macromolecule is dynamic, but I am specifically avoiding exceptions to the rule to avoid confusing the issue.

The helical structure of DNA is a low energy form which makes its formation thermodynamically favourable. Chemical bonds in DNA (and every molecule) have conformational flexibility which means that the molecule as a whole can adopt different structures. If you picture two DNA strands joined by hydrogen bonds but in a non-helical, straight form, you can simply twist the strands about their central axis to form a helical structure. This twisting is allowed because of the conformational flexibility of the chemical bonds. The helical structure is more stable than the "straight" form (because of base stacking interactions), and so it forms spontaneously. I struggled in vain to find a good animation of this, but came up short. You can skim through this video to see an example of what I'm talking about. It's subtle, but you may be able to see, or conceptualize, that as the two strands are twisted around each other, the adjacent bases in a strand come closer together. This permits stabilizing interactions between the adjacent bases which favours spontaneous helix formation (I briefly discuss this at the end of another answer).

As for how frequently the "rungs occur", this is dependent on the specific helix geometry. In B-form DNA, the geometry thought to occur predominantly in vivo, the helix completes one full turn approximately every 10.5 bases and the spacing between adjacent bases is ~3.4 Å, as shown below:


Why do flies "rub" their front legs when resting? I've noted that every time a house fly is resting on a surface, it appears to "rub" or "scrub" its front legs in a repetitive movement. And they do it continuously. Why?

Flies rubbing their legs are cleaning themselves. They can also often be seen rubbing their back legs often. Additionally, flies also often clean their wings, compound eyes and bodily bristles. Legs and wings are used as a primary means of locomotion and means of escape. Eyes and bristles are sensory organs and hence also essential for their survival.

Below a picture of a tachinid fly showing the bristles and compound eyes:

The eyes need to be clean as they are essential for the detection of visual stimuli. The bristles, as a commenter rightfully stated, contain chemoreceptors reminiscent of receptors on the human tongue that sense sweet and bitter tastes. These taste receptors alert the fly for sweet (food) and bitter (poisons) substances. Hence, cleaning of the legs may not only serve hygienic purposes, but may well be important for keeping the bristles and hence the associated sensory organs clean and free of prior encountered substances.


Antigenic and non antigenic Can any foreign molecule be non- antigenic ? Can any foreign peptide be non-antigenic ? What is the difference between an antigenic and a non-antigenic peptide ?

Something is antigenic because it acts as an antigen - it binds to an antigen receptor in the immune system (antibody, B-cell receptor, T-cell receptor, etc.). While the concept of "foreign" in immunology is often (incorrectly) equated with antigen, that is not the case. For example, there are many chemicals one could think of that are foreign (non-self), but don't usually raise immune responses - nylon, for example.

The difference between an antigenic and non-antigenic peptide is that the antigenic peptide, when presented in the correct circumstances, can raise an immune response. This means that, theoretically, the exact same peptide sequence can be both antigenic and non-antigenic depending on the environment - whether it's being presented in an immune-suppressed environment, for example. However, it's more common to classify antigenic potential based on whether it's possible for the substance to raise a response in an otherwise "normal" immune environment.


Hormonal effects of Luteinizing hormone on endometrium What is the effect of luteinizing hormone on the endometrium?
A general answer to this query is that it only thickens it. The same could also be said for the effect of Follicle stimulating hormone (FSH) on the endometrium as well.
Where lies the difference?

Both FSH and LH are indirectly involved in endometrial thickening:

GnRH regulates release of the gonadotropins- luteinizing hormone (LH) and follicle-stimulating hormone (FSH) from specialized cells (gonadotropes) in the anterior pituitary gland
LH and FSH promote ovulation and stimulate secretion of the sex hormones estradiol (and estrogen) and progesterone from the ovaries.
As estradiol levels increase, the intact basal layer regenerates the endometrium to its maximum thickness late in the ovarian follicular phase (proliferative phase of the endometrial cycle).     ...{1}

Again, wikipedia{2} says the same:

...In both cases, the endometrium initially proliferates under the influence of estrogen.

The difference between the hormones, of course lies in their other functions. You can see this for more on that. To clarify again, the endometrium does not thicken 'differently' under the influence of each.
{1}-https://www.msdmanuals.com/professional/gynecology-and-obstetrics/female-reproductive-endocrinology/female-reproductive-endocrinology?query=lh
{2}-https://en.wikipedia.org/wiki/Endometrium#Cycle


Which will produce more oxygen? A few large trees or a greater number of smaller plants? In a given area A, we have two choices -
(i) we can plant maximum number of trees (which are larger in size) possible in A, say m
OR
(ii) we can plant maximum number of plants (which are smaller in size) possible in A, say n
(evidently m will be smaller than n)
Which choice will yield more amount of oxygen?
It can be assumed that the total number of leaves capable of Photosynthesis is N and is same for both the cases.

Ignoring parameters such as:

Leaf shapes
Difference in photosynthetic efficiency due to other metabolic factors
Unequal illumination of leaves
Nutrient content of the soil

Photosynthesis rate of a plant1 depends on the [total number of leaves] × [surface area of a leaf].

Assuming that a tree occupies same ground area as a shrub, there will be same number of trees as shrubs.

A tree is taller and can bear more number of leaves and if we assume that the surface area of the leaves are similar between trees and shrubs then the tree would carry out more photosynthesis.

However you say that the number of leaves is the same; in this case both will carry out same amount of photosynthesis (the shrub may outlive the tree though, as the latter won't be able to support its huge size with same level of photosynthesis as the shrub).

A note on phtoplanktons and algae: One reason amongst a few for why they are efficient at photosynthesis is because the number of photosynthetic cells per volume is higher in them.

1 I am using the term plant to denote all plants. Big trees are called trees and small plants are called shrubs, for convenience.


One Sample, Different Methylation Values I'm hoping that somebody here can explain this unusual result that I'm getting with some pyrosequencing data. I have bisulphite converted a few samples a couple of times over the years for different projects. Recently I was collecting some of this disparate data together and I noticed that when the same pyrosequencing assay was used on these samples, those that were converted later had decreased methylation at the CpG sites of interest compared to the initial bisulphite converted samples. The original conversion was in 2010 and the repeat conversions were in 2014/2015. The assays are the same and it's difficult to blame this on PCR amplifying one clone over another since I've done technical replicates on each aliquot. Even the 2010 converted sample has the same result in 2015 that it did in 2010 but this is different from the 2015 converted sample.

We are using the same kit (Qiagen) for bisulphite conversion and haven't made a major change to our procedure (we follow the Qiagen protocol without modification). Has anybody noticed this phenomenon before? Is it possible that stored DNA would experience methylation changes? It seems more likely that the issue is technical but I'm having trouble figuring out exactly what that technical issue is.

I looked into this and if the effect is real, which it sounds like it is, it may be 5-formylcytosine.

Methylcytosine oxidizes into hydroxymethylcytosine, which reacts with bisulphite exactly like you expect (identically). Hydroxymethylcytosine further oxidizes to 5-formylcytosine, which behaves like unmodified cytosine (i,e. deaminates to form U). TET enzymes mediate this behavior in vivo but I can't find any data on spontaneous methyl group oxidation or what the kinetics might be like. This paper relies on the properties of 5-formylcytosine outlined above.

You could use this paper to test if that's true. Reduction with sodium borohydride converts 5-formylcytosine back to hydroxymethylcytosine, which reads as methylated under bisulfite sequencing.


Is there a period after you have had a cold when you cannot get a cold again? I always assumed colds ran on a 'no tagbacks' principle: once it's out of your system, it takes a while before you can get a cold again. Is there any truth to this, or can rhinoviruses hit you at any time?

The short answer is no, there is no minimum time between two colds. The reasons for this are different.

Mostly it has to do with the viruses which cause the common cold. There is a bunch of them causing what we call a cold, including rhinoviruses, coronacviruses, adenoviruses, human parainfluenza viruses, human respiratory syncytial virus, enteroviruses other than rhinoviruses and metapneumovirus. As much as 200 different virus serotypes are connected to this disease, alone 99 from the rhinoviridae. See the references 1-3 for more details.

Different serotypes means that two viruses of the same family (a rhinovirus for example) have different surface antigens on the virus and are not recognized by the same antibody. And this is what makes it difficult for the immune system. When it has learned to recognize and defeat one virus which causes a cold, it still has to learn how to do this with another (serotypically different) virus. So the adaptive immune system has to make highly specific antibodies every time it is faced with a new virus (which is of course not limited to cold viruses).

Once you have been infected with a virus and developed a sufficient immune reaction to develop antibodies, you are usually immune against this specific virus (with its specific serotype). Cold viruses live in communities, so when you move or travel, you will most likely encountered with different viruses, which your immune system doesn't know...

Finally there is another point which adds to the problem: Mutations of the viruses. The viruses are mutating constantly (RNA viruses at high rates) which changes their appearance and also their surface molecules (which are important for the recognition through the immune system). This leads to new serotypes, which are unknown to the immune system. See reference 4 for some more details.

References:

Understanding the symptoms of the common cold and influenza.
Sequencing and analyses of all known human rhinovirus genomes reveal
structure and evolution.
Common cold
Mutation rates among RNA viruses


Do all restriction enzymes have palindromic recognition sites? I am trying to find out the requirements for a segment of DNA to be the recognition site of a restriction enzyme.

Acording to the article on Restriction Enzymes in Wikipedia, "many of them" (referring to recognition sites) are ‘palindromic’ (in the sense that the sequence of nucleotides on one strand should read the same as the that on the other strand, from the opposite direction).

Is this true for all recognition sites?

The article cited in the question goes on to discuss the different classes of restriction enzyme, for which the recognition ‘style’ differs. Not all recognize palindromic sequences.

Type II restriction enzymes

These have been divided into a number of subclasses (reviewed by Pingoud and Jeltsch). Those regarded as orthodox — which are the ones generally used in DNA cloning — appear always to require palindromic sequences in their recognition sites, although those in some other classes do not (see list here).

This statement is subject to the proviso that you regard as palindromic 5-base recognition sites, such as AlwXI, GCAGC, and others with a ‘non-conforming’ central region, such as ApaBI, GCAN5TGC. The reasons for including the latter (which provides an alternative way of defining the requirements of the recognition sequence) can be seen by examining the symmetrical manner enzymes of this class bind the site, which can tolerate a non-symmetrical central region. This is described in more detail in an answer I gave to another SE question on restriction enzymes.

Type I restriction enzymes:

  …cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions—one containing 3–4 nucleotides, and another containing 4–5 nucleotides—separated by a non-specific spacer of about 6–8 nucleotides.

Type III restriction enzymes:

  …recognize two separate non-palindromic sequences that are inversely oriented. They cut DNA about 20–30 base pairs after the recognition site.


How can antibodies in rapid antibody tests be kept at room temperature without denaturing? The normal temperature for long term antibody storage is around -20 degrees Celsius. However, when developed into rapid antibody tests, they can be kept at room temperature for prolonged periods. How is that possible?

Antibodies have no problem with room temperature. Naturally, antibodies expect to survive for many days or weeks at body temperature, which is much higher than room temperature (at least, mine is).

-20°C is recommended for very long-term storage (many months or years) of antibodies, but they are typically very stable proteins and don't denature very readily at all. Storing them at room temperature can be done for a long time -- certainly weeks, in my experience, with the only real concern being the possibility of bacterial or fungal growth if the antibodies aren't sterile.


Why is it thought that protein folding is determined solely by amino acid sequence? It seems that it is a generally accepted idea that protein folding is completely determined by the sequence of amino acids, but why do people believe that? Is it simply that no example of a protein with two different functional foldings (possibly with different functions) is known, or is there some theoretical reason that it would be impossible for such a protein to exist?

This question is, in my opinion, based on an incorrect premise but nevertheless throws up a number of points about protein folding and protein structure that can be addressed, albeit briefly.

The False Premise

  “it is a generally accepted idea that protein folding is completely determined
  by the sequence of amino acids”

(My emphasis.)

No…

What is thought to determine protein folding?

The basic principle thought to be the main determinant in protein folding is thermodynamic. If possible†:

  “A protein will fold so that the whole system of which it is a component is
  in the state with the lowest Gibbs Free Energy”

Thus, the protein itself is a major contributor — but not the sole contributor.

There is no argument that amino acid sequence (and composition) will be an important determinant of the contribution of the protein to the thermodynamically most favourable state, as the chemistry of the amino acid residues determine how it can interact chemically with its environment (albeit with weak interactions) and how it may interact with itself to produce a conformation which may have an appropriate effect on the entropy of the whole system.

So this is viewpoint is based primarily on chemical thermodynamic assumptions, rather than special ideas of molecular biology. An elementary exposition of this idea can be found in Berg et al. Section 1.3.4.

How can the environment affect protein folding?

One major influence is whether the protein is in an aqueous (hydrophilic) environment, like the cell cytoplasm, or a non-aqueous (hydrophobic) environment, like the cell membrane. In the former environment a protein will fold so as to expose its hydrophilic residues to the environment, in the latter its hydrophobic residues (discussed, in this paper, for example). Or it may be unable to fold at all in the wrong environment.

Another influence on the folding of a polypeptide chain may be the presence of another polypeptide chain with which it can interact, as in the case of the alpha and beta subunits of haemoglobin (see the classic paper by Perutz (1970))

Small molecules can influence the structure of a protein such as in the case of 2,3-diphosphoglycerate (2,3-BPG) on haemoglobin mentioned below.

When a protein is synthesized in an environment unconducive to correct folding it may require a chaperone protein to transport it to an appropriate environment.

And if the final structure of a protein requires covalent linkages, e.g.  between the SH groups of cysteine residues, an enzyme is need to oxidize them.

What evidence do we have for this?

We have evidence that some proteins that have been unfolded by putting them in environment that is thermodynamically unfavourable to their native (end enzymatically active) structure can refold when the environment is slowly returned to one that is favourable. This is the famous Anfinsen experiment with ribonuclease (described in this book section). Important as this experiment was in supporting the thermodynamic idea and showing that the contribution of the protein was inherent in its own composition,  it does not prove that this is what happens in vivo, nor that the structure formed is the one with the lowest thermodynamic free energy.

The importance of individual amino acids in the sequence is attested by examples such as the mutation of a single amino acid in beta-globin in sickle-cell anaemia (glutamic acid to valine). Under certain circumstances this allows the haemoglobin molecules to polymerize into long fibres because of the interaction of the hydrophobic valine residues with residues in  another subunit rather than with water.

Different states of folding are possible in a single protein

This addresses the section of the question regarding a possible:

  …example of a protein with two different functional foldings

There are many so-called allosteric proteins that are regulated by interaction with small molecules (their environment) which cause a shift from one conformation to another. The example par excellence is haemoglobin, which is in an equilibrium between two states that are influence by the binding of oxygen, hydrogen ions (i.e. the acidity of the blood) and 2,3-BPG.

Another type of example is the shift that can occur between the secondary structures producing amyloid proteins.

†Can we be sure that a protein always adopts the structure of the lowest energy?

No.

The manner in which a random coil is a highly complex field, but, in brief, one can imagine that the path to the structure of lowest energy is blocked in some way (an energy barrier that would have to be overcome, perhaps) so that the structure adopted is, instead, the lowest attainable in practice.

[A rugged energy landscape with hills, traps and energy barriers and some narrow throughway paths to native — from Dill & Chan, 1997]


Why are there two mature sequences of microRNAs in miRBase entries? In the miRBase database entries generally show a stem loop sequence and two mature sequences. For example the entry for hsa-mir-15a gives three sequences: (1) the Stem-loop sequence hsa-mir-15a, (2) Mature sequence hsa-miR-15a-5p, and (3) Mature sequence hsa-miR-15a-3p.
What is the difference between the two mature sequences? Does the stem loop structure divide into two different miRNA species?

I am not sure whether it is made clear in the Wikipedia article on microRNAs, but, yes, there are two possible mature mir species that can be generated from the stem-loop precursor — one from each side of the stem — although most often one greatly predominates.

The diagram in Wikipedia shows the generation of a single miRNA:

However, the entry mentioned in the question (hsa-mir-15a) shows that although the 5′-stem component (UAGCA…) is most abundant in this case, there is a small amount of the 3′-stem component (CAGGC…).

In Drosophila melanogaster a single stem component (more often from the 3′-stem, but also from the 3′-stem) most frequently predominates, but I have personally found microRNAs in which both components occur in similar amounts (unpublished).


A synthetic sieve organ known as kliver? in this video at 5:28, the narrator talks about a "vat-grown all-purpose sieve organ" called Kliver that would do away with both liver and kidney transplant. But i don't seem to find online resources about the same. Is that terminology popular in scientific literature, and if so, how would synthetic biology accomplish that? articles about the same will also be appreciated.

This term is used in this book (Synthetic Biology, The National Academies Keck Futures Initiative, p.43). This book is a summary of several interdisciplinary team discussions during a  conference held in 2009.

One...

  [...] team considered building artificial organs. Engineered to be hypoallergenic, these could allow for a mass production of personalized organs. Their novel and broad functions could also be useful for medical testing. In a single artificial organ, one might screen potential drugs for both toxicity and permeability.

  For instance, group members proposed the idea of a "kliver", a kidney-liver hybrid. An independent "kliver" could help filter bio-compounds out of drinking water.

There are some more paragraphs revolving around the question how to build a "kliver" and a final paragraph concluding that enough necessary building blocks were available and researchers could start working on it:

  Potential building blocks might be mammalian and microbial cells and their products, such as slime, fibers, small molecules and proteins. The cells might be engineered to hold new electrical, mechanical, and chemical powers.
  [...]
  Cells would be programmed to degrade their organs and DNA if they began to invade other organisms or the environment. A genetic "kill switch" aims to stop contamination or infection.

Summarising this, I wouldn't call it a "popular term".


parallels or replicates? I am writing an article where I describe real-time PCR experiments. My collaborator, after reviewing the article, consistently replaced the word "parallels" with "replicates". Are they not synonymous?

I prefer the word parallel, because, in the context of PCR, it implies that these three identical experiments were performed in the same real-time PCR run (and not consecutively).

The explanation I got when learning how to do qPCR was that you need run both replicate experiments and parallel experiments to get publishable data.

Replicates (or biological replicates) would be qPCR runs on independently collected samples. That does not count your control vs your experimental groups. So for my work I had to collect 3 sets of control tissue and 3 sets of experimental tissue from independent sets of animals (in my case 3 generations but for mammalian work I think three different animals would be ok).

Parallel does imply that you ran the the samples together in the qPCR machine. I think the standard is that for each sample in a particular replicate you need to run three qPCR reactions in parallel. So in total you need to run 9 wells of qPCR reactions for each test group.


Are there special constants in biology that define organism's morphology? In math, there are special numbers, like Pi (3.14159...) and e (2.71828...). In chemistry, there's numbers like avogadro's number (6.0221413e+23). For example a circle can be defined in terms of 2 * Pi.

Are there any significant constant numbers in biology that define the shape of an organism (ex: mammal)? I'm talking about stuff like shoulder to hip ratio or length of an organism, etc?

Here's an example that came to mind - different fetuses developing into different organisms. Is there any constant that is the same for these at some stage of development? Like the ratio of head to tail?

I don't know if this is what you mean, but take a look at BioNumbers.

Also, mathematical constants like pi are different from physical constants. Mathematical constants are true in a mathematical (logic) sense, and do not need to be related to any physical quantity. They are derived by logic. Physical constants, on the other hand, typically describe an observed relation between two types of quantities. They are derived by measurement.


Adaptability in immune system I read somewhere that recently some people are trying to use harmless bacteria that live symbiotically in humans to express some portions of antigens of the harmful ones. Some people have raised concern that continuous exposure to the same antigen may lead to adaptibility of immune system to that epitope and render it useless when the germ actually comes.

Can't we use the same procedure for exposing some parts of MHC of the donor to the recipient before transplantation, so that, by the time the real transplant is done it may become adapted ? How much time would it take for this to occur ?

I can already see one drawback : In emergency transplants, this can not be used due to time factor. Can you see any other drawbacks ?

No. MHC works differently from any other antigen. MHC is involved in the maturation of T lymphocytes in the thymus. Forming lymphocytes need to recognise the MHC with a certain affinity (lymphocytes with too much affinity for the MHC are destroyed). In all this process there is no intervention of foreign antigens, so the system you propose won't work because the lymphocytes would search the MHC of the graft and they would attach them with abnormal affinity. This would trigger autoimmune response.

What you propose is the main functioning of allergy vaccines. You expose the immune system to low dose of antigen during long time, and that would make the body to not react aggressively to the substance. However, this phenomenon is based in B lymphocytes, which recognaise soluble antigens and little cells (humoral immune system) instead of whole cells (cellular immunity).

In the domains of science fiction, however, it would be technically possible to transfect thymal cells in order to express the MHC of the donor, since it would express both. Actually, this should be theoretically easy (The thymal cells seems to express almost any protein in the body, in order to prevent autoimmunity), but it face the problem of thymal degeneration.


Does the corpus callosum have a significant relationship with motor memories/ muscle memories? With the corpus callosum located in the cerebrum, and motor memories having a closer relationship to the cerebellum (which I'm not quite sure about), is there a significant relationship between the corpus callosum and motor memories? Do motor memories process in one hemisphere and are then shared with the other- if so, how? Thank you so much for your time and patience!

This study tests the time it takes for patients with damaged corpus callosums to perform intermanual transfer motor tasks.
Patients drew a meaningless figure with one hand, then did it again with the other hand (And vice versa). Thus performing intermanual transfer.

All three patients displayed a significant benefit for transfer from the dominant to the non-dominant hand but not vice versa during proximal motor activity.

...the proximal transfer behavior was found to be similar for all patients in the healthy group.

From these results, a relationship exsists.


Difference between LH and ICSH Are Luteinizing hormone and Interstitial Cell Stimulating Hormone(ICSH) the same?

As far as online dictionaries (Medical Dictionary, Merriam-Webster) and a popular-scientific site on hormones (Your Hormones) go, LH and ICSH are the same. ICSH mainly pops up in the older literature; e.g., Lostron & Johnson (1966) and Louvet et al. (1975). My understanding is that LH is currently the more accepted term for the hormone.

I get the impression that historically, LH has been used in relation to female reproduction and ICSH to the male reproductive systems. In males, LH stimulates Leydig cells in the testes to produce testosterone. In females it stimulates the ovarian follicles to produce oestradiol, and it induces ovulation.

References
- Lostron & Johnson, Endocrinology (1966); 79: 991
- Louvet et al. Endocrinology (1975); 96(5): 1179-86


Looking for a cancer drug target database to guide sequencing of patient tumor DNA I have a question I would like to pose to the community. I have recently received access to a bench-top ion torrent DNA sequencer. Our idea is to use this machine to sequence the DNA from patient’s tumors in order to guide treatment options. My job is to identify a list of all currently used anti-neoplastic drugs along with their known targets (i.e., specific genes and mutations) and accession numbers. I would like to put these data in a table in which each row corresponds to a different drug.

For example, a row in the table might read (column names are indicated in brackets): [disease] breast cancer, [drug] trastuzumab, [drug target] HER2/neu receptor, [gene] ERBB2, [location] chr17:37844393-37884915, [mutation type] amplification, [accession number] ENSG00000141736. The pathologists would then be able to use this database in order to select appropriate genes for sequencing whenever they receive a tumor specimen. If the patient’s tumor had an amplified ERBB2 gene, they could be given trastuzumab.

Currently our study is in pre-planning stages (i.e., we won’t actually be testing this on patients any time soon). I would appreciate it if anyone could give me on advice on how to go about creating such a database. I am aware of online databases including COSMIC, Sanger's Cancer Gene Census, and the Potential Drug Target Database (PDTD), but they don’t have everything that I’m looking for. I am familiar with R and could use it to combine data from multiple sources if necessary. If anyone else has comments or suggestions for further reading that would also be appreciated. Thanks!

Note: This question has also been posed on a Research Gate forum: http://www.researchgate.net/topic/Cancer_Biology/post/Looking_for_a_cancer_drug_target_database_to_guide_sequencing_of_patient_tumor_DNA

Not sure if the exome sequencing is the way to go for this kind of tasks, especially if you have an idea of the mutations you might be looking for. Current arrays are pretty performant and are much more rapid and cheap.

For the data, you might consider having a look on The Cancer Genome Atlas. Otherwise Biological Networks might provide you the API for you if you aren't afraid of doing a little bit of Java to interface it with R.


What does fluorogenic mean for fluorescent probes? Many fluorescent probes are described as being fluorogeninc as an advantage for fluorescence microscopy but what does fluorogenic mean? Dictionary definitions state that it means generating fluorescence, but i've read somewhere that it involves switching the fluorescence on or off for super resolution microscopy. I just want to understand the exact meaning in this context. Thanks in advance for the help.

The usage of "fluorogenic" is typically applied to probes that are not currently fluorescent but can be, typically by some enzyme action or other reaction. For example, see here, here, or here. Essentially they are precursors to the fluorescent molecules of interest.

As one example, you could get a higher signal to noise ratio if you only "activated" the fluorogenic compound in one area, perhaps inside cells vs in the extracellular space, for example, so you aren't dealing with stray light from that "unwanted" signal.

References:

Shieh, P., Hangauer, M. J., & Bertozzi, C. R. (2012). Fluorogenic azidofluoresceins for biological imaging. Journal of the American Chemical Society, 134(42), 17428-17431.

Lukinavičius, G., Reymond, L., D'Este, E., Masharina, A., Göttfert, F., Ta, H., ... & Blaukopf, C. (2014). Fluorogenic probes for live-cell imaging of the cytoskeleton. Nature methods, 11(7), 731-733.

Friscourt, F., Fahrni, C. J., & Boons, G. J. (2012). A fluorogenic probe for the catalyst-free detection of azide-tagged molecules. Journal of the American Chemical Society, 134(45), 18809-18815.


Is it dangerous to eat a mutated eggplant descended from a radioactive ancestor? What is the risk, if any, associated with eating a 100th-generation mutated eggplant derived from a radioactive ancestor?

In another word, is that possible that organic toxin will be produced by the mutated plant and is it a good idea to plant it in America? These plant seems very beautiful to me! Ha Ha

Note: The descendant eggplant is not radioactive.

Motivation: There are many mutated eggplants around Japanese power plants.

While it's always possible that a mutated eggplant will produce a new toxin, this is very unlikely. I don't know how much higher the mutation rate is near Fukushima than in general but the difference can't be huge. Even if it's, say, 5 or 10 times higher than normal (I'm making up these numbers), the risk is still tiny. Actually, plant breeders sometimes use radiation to produce more variety to work with and we don't worry about that.


What are the predators of Glaucus atlanticus? I'm researching the Glaucus atlanticus, also known as the blue glaucus, among various other names, but after reading quite a few articles and searching on the Internet as many different ways as I can think of, I can't find any of its predators, or any indication it has no natural predators. Everything I've read is just silent on the issue. Does anyone know what, if any, predators this has? Thanks!

Try out using Google Scholar to take a more scientific literature-based approach to your search.

Frick et al. (2009)1 found that about 42% of logerhead sea turtle (Caretta caretta) stomachs contained remnants of G. atlanticus.

  We were able to identify G. atlanticus in the diet of loggerheads because whole or nearly intact specimens were present.

 Loggerhead turtle mouth and throat with sharp papillae. Source NCSU CMAST (Photo by Craig Harms)

Bieri (1966)2 observed G. atlanticus frequently attacking one another and biting off pieces of each other. In one case, one individual ate all but the head and trunk of a smaller specimen.

Citations:

 1, Frick, M.G., Williams, K.L., Bolten, A.B., Bjorndal, K.A. and Martins, H.R., 2009. Foraging ecology of oceanic-stage loggerhead turtles Caretta caretta. Endangered Species Research, 9(2), pp.91-97.

2. Bieri, R., 1966. Feeding preferences and rates of the snail, Ianthina prolongata, the barnacle, Lepas anserifera, the nudibranchs, Glaucus atlanticus and Fiona pinnata, and the food web in the marine neuston.


What actually happens when my leg 'falls asleep'? Most people have experienced the temporary loss of feeling and tingling in their leg resulting from sitting in an abnormal position for a short while. Usually you get a loss of feeling in your leg while it is being compressed/constricted at some point and then the tingling sensation as the pressure is removed. But what is actually happening? I understand the the blood vessels are probably constricted from the pressure, but how does this lead to loss of feeling and later the strange tingling sensation? Are there any other things that extended compression on the leg does to cause this? What exactly are the requirements to get the sensation of a one's leg or other limb falling tingling in that manner?

The feeling you describe is called "paresthesia," and according to the NINDS info page, it happens "when sustained pressure is placed on a nerve."


Does the number of nodes determines the rate at which a neural signal is transmitted? I know that the the bigger the neuron's diameter is, the faster the neuron signal is transmitted. This makes sense according to the proportionality of resistance to the inverse of area and thus, in physics, there is lower resistance in wires that have bigger diameters (cross-sectional areas). I can imagine that this is the same logic for our neurons as well because they are like wires. I also know that the more myelinated a neuron is, the faster the neuron signal travels too because myelination acts as an insulation that reduces resistance in signal transmission.

But then, my question is: does the number of nodes matter and affect the rate at which a neural signal is transmitted? Can you please help explain why or why not? Let's say for example, that two neurons have same amount of diameter and myelinated sheaths hypothetically, but one of them has more nodes. Does that number of nodes of ranvier make the saltatory conduction faster?

The number of nodes is a trade-off between speed of conduction and reliability. The fastest transmission would be where nodes are spaced at roughly the maximum distance to trigger sufficient depolarization at the next node - however, small changes in ionic concentrations or channel densities could lead to failures, so in practice the nodes are typically a bit closer.

The slowest transmission would be to have no saltatory conduction at all.

(I mean these to be general principles; one could probably design a hypothetical system with very close nodes that is actually worse than having no saltatory conduction, and there is probably a perfect edge case where nodes that are spaced at the maximum distance are slower because of membrane time constants)

The reasons for this are: that travel between nodes is very fast, regeneration at nodes is comparatively slow. However, there is a maximum distance for reliable transmission, so we can't simply have one long stretch containing no nodes in between.

edit: references were requested. This was off the top of my head so I would suggest any introductory neuroscience textbook, Purves is a preferred one of mine, but this will run you significant $ if you are not/have not been a student in a neuroscience course. The Wikipedia articles for https://en.wikipedia.org/wiki/Node_of_Ranvier and also for Saltatory Conduction both look good to me, though they do not address the specific issue in detail. This brief Neuron review is more appropriate to the specific question asked, though I am not sure people without an academic library subscription will have free access: http://www.sciencedirect.com/science/article/pii/S0896627300803232


Measuring protein concentration, Bradford vs. Nanodrop? I know that the bradford assay is a very standard way of measuring protein concentration after e.g. a purification. However, in the lab that I work in now they normally only use nano drop at the 280nm wavelength.

How trustworthy is this concentration? Say that I e.g. get 2.5 mg/mL, could I really trust this?

That depends strongly on your protein and how exact you need this concentration. Both tests (Bradford and the measurement at 280nm) only do an approximation.

The measurement at 280nm relies on the interaction of aromatic aminoacids with the UV light. If you have a protein with few or no aromatic amino acids, your measurement will be wrong.

The same is true for the Bradford assay. Here you form a complex between Coomassie Brilliant Blue and unpolar and cationic side chains of the amino acids. This test is more precise, since it includes more possible side chains, but is still dependend on the composition of the protein.

More precise is the BCA assay, since it utilizes the reduction of copper ions by the peptide bond of the protein.
What you could do is run a BCA assay (or at least a Bradford assay) from your sample and measure the same sample on the Nanodrop at 280nm and compare the results.

You can find an overview over the methods here and here.


Effects of HRT on transgender(M to F) physiology and athleticism. I often heard of athletes in the Olympics who would be accussed of having an advantage because they were intersexed.

Now I know transgenderism and being intersexed are not the same thing, but they can both involve Hormone replacement therapy.

Therefore would a transgender women (ie: a person assigned male at birth, who transitioned to female) have advantage over cisgendered(not transgender or intersexed) women in sporting events due to anatomy or physiology from previously having a male form?

To add detail, I guess it would depend on the state of their transition, so one could use MMA competator Fallon Fox, as an example, or any other transgender women.

My thoughts on the effects of HRT on athleticism for transgender people is that if they were more advantageous, then they should be dominating their respective fields.

As for the biology, I know that bone growth stops at around 20, but how would the HRT affect their muscles, and would muscles even matter without the corresponding frame?

.

We have two groups of people or better to say scientists and specialists that have their own ideas and theories and approvements.

People that are relay on genetic related ideas that mostly consider rule of Y chromosome on men and how some genes' rules will not be diminished only by hormone therapy or non genetically engineering methods.

Case example:

  Chloie Jonsson, 34, who transitioned more than eight years ago, is legally recognized as female in the state of California. Despite the medical community's consensus that transgender women do not have a competitive advantage over cisgender (nontrans) women, Jonsson's application to participate in CrossFit's women's division was rejected with a bizarre letter claiming she and her supporters do not understand "the human genome" and "fundamental biology." In response, Jonsson filed suit against the fitness giant.

  The letter from CrossFit general counsel Dale Saran reads:

  "We have simply ruled that based upon [Chloie] being born as a male, she will need to compete in the Men's Division. The fundamental, ineluctable fact is that a male competitor who has a sex reassignment procedure still has a genetic makeup that confers a physical and physiological advantage over women. ... Our decision has nothing to do with 'ignorance' or being bigots — it has to do with a very real understanding of the human genome, of fundamental biology, that you are either intentionally ignoring or missed in high school."
  Later, Saran disputes the statement made by Jonsson's attorney that "by all accounts, both physically and legally, Chloie Jonsson is a female."

  "This is simply wrong as a matter of human biology and if you can't see that, there really isn't much to talk about," writes Saran, citing Encyclopedia Britannica. "Chloie was born, genetically — as a matter of fact — with an X and a Y chromosome and all of the anatomy of the human race. Today, notwithstanding any hormone therapy or surgeries, Chloie still has an X and a Y chromosome."

To add some details to group one's idea, if you think of some genes and their rules in men that makes them more accurate and more muscular than women in the field of physical activities, you'll get to the point of how to control or change behaviour of these genes in the body of a man to make him woman, both muscularly and neurologically which is not possible for now because we need some very detailed and powerful calculations to know the exact equilibrium of a man genome as if he was a woman.

To change the complicated mechanism of Y chromosome on Biochemistry and behaviour of other chromosomes we have so much to learn and we need very fast computers to simulate the behaviour of molecules and new formation of mass body.

And we have other ideas by people who insist on level of hormones that has a great effect on mass of bone and muscles in men and women regardless of how their sex and genome is.

Case example:

  Eric Vilain, Director of the Center for Gender-Based Biology and Chief Medical Genetics Department of Pediatrics at UCLA, says of any perceived advantage a transgender woman may have, “Research suggests that androgen deprivation and cross-sex hormone treatment in male-to-female transsexuals reduces muscle mass; accordingly, one year of hormone therapy is an appropriate transitional time before a male-to-female student athlete competes on a women’s team."

A great article and detailed explanation by an example that helps to answer your question is here.


What is the difference between Ostracodermi and Placodermi I looked the word origin and found Placodermi is PLATE SKINNED while Ostracodermi is Shell Skinned.
Can someone please explain the difference between being Plate skinned and Shell skinned?

If in reference to the prehistoric groups of fish of the respective classifications, ostracoderms would have had a bony head much like a shell, and placoderms had articulated plates covering the head/thoracic area. The differences are relatively straightforward, see the wikipedia pages for each:

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

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


How much vitamin C has a noticeable effect on E.coli k12 I am doing a research on effects of different concentrations of vitamin C on serial dilutions of E.coli k12. I am looking for literature that has already shown effects of vitamin C on E.coli, but there is a vast amount out there (26 thousand Scholar hits).

What might be the main effect of Vitamin C on E.coli? Is 1000mg vitamin C enough to have noticeable effects on the bacteria?

I found a 'short communication' paper by Akira Murata et.al where they did In Vitro testing of Vitamin C on L. casei showing no inhibition of growth, and also tested on E.coli and B. subtilis and found that Vitamin C inhibited the growth. Also I believe Suzanne Humpries stated the same thing somewhere in this 1.5 hour long video, indicating she may posses more knowledge as to studies.

  Ascorbic acid did not inhibit the growth of L. casei even at high
  concentrations, and rather stimulated the growth at certain
  concentrations (2~3 X 10- 2 M). This observation indicates that
  ascorbic acid can be used as an antiviral agent.

  In E. coli and B. subtilis, unlike L. casei, a high concentration
  of ascorbic acid acted so as to lessen their growth rates (Fig. 3).
  Particularly, in B. subtilis W23, cell lysis was observed about 100
  min after the contact with ascorbic acid and, moreover, when a drop of
  the lysate was placed on a plate seeded with B. subtilis 168 and
  incubated overnight at 30oC, there appeared a clear zone around the
  placed lysate. Since B. subtilis W23 is known to possess an inducible
  defective phage PBSZ able to kill B. subtilis 168,3 ' 41 the observed
  result maybe ascribed to the induction of the defective prophage from
  B. subtilis W23 by action of ascorbic acid. Lwoff and Siminovitch51
  reported once that the lysogenic phage in B. megaterium was induced by
  treatment with ascorbic acid.