Translation of Poly-U in the Nirenberg and Matthaei experiment In the Nirenberg and Matthaei experiment the artificial mRNA, polyU, was translated into polyphenylalanine in a cell-free system, establishing that UUU was the codon for Phe. How did this work as the artificial mRNA lacked an AUG initiation codon, which we now know is required for translation of cellular mRNAs?

This is an intelligent question that highlights the ‘sleight of hand’ simplifications employed in many text books to make experimental science appear cleaner and more logical than is in fact the case. From what we now know about the requirement for an AUG initiation codon in protein biosynthesis these experiments should not have worked.

The reason they did was that they were performed at an unphysiologically high concentration of Mg2+ which overcomes the need for specific initiation (and, incidentally, allows other reactions of protein synthesis to proceed in an abnormal manner, particularly the codon-directed tRNA binding reaction used to finish the deciphering of the genetic code). You should also bear in mind that the efficiency of the reaction was probably much less than that within the cell, but this was of no concern as all that was required was that a product be synthesised.

Reference

I worked in this area in the late 60s/early 70s and the importance of magnesium concentration was just common knowledge in the field, so it is difficult to cite a reference to support my assertion. However a brief search brought up a contemporay paper on the effect of magnesium on initiation of protein synthesis in phage RNA, illustrating its importance. There are, no doubt, others.


How long can a naked human survive on Mars? How long can a naked human survive at the surface of the Mars planet?

For instance, let's say a worker's base takes fire while he sleeps, the building is totally ablaze and he can do nothing but run to the emergency building 200 meters away without any respiratory equipment, pressure suit, UV protections or anything.

Maybe a human could survive for a rather long time, and apnea time is the real limiting factor?

Climate:

Temperature: 27 °C to −50 °C (base is at a rather warm location, on Equator)
Pressure: 0.006 bar (Earth: 1 bar)

Long story short, the astronaut probably wouldn't make it, and would first loose consciousness then suffocate.

There is a lot of myth and hollywood dramatization regarding this kind of thing. Here are some:

You will explode. This is just ridiculous. The skin is air tight (relatively speaking). It is also very elastic and can pull and bend quite a great deal before tearing. Through quite a few, equally durable, tissues, it is connected to the bones, which are unaffected by negative air pressure.
Your blood will boil. The circulatory system is also a closed system. It is not directly exposed to the environment. Also, the blood pressure in a healthy person is averaged around 100 mmHg and Earth's atmosphere at sea level is 700 mmHg. There is already a massive disparity, yet Earth's atmosphere doesn't go pouring into our veins at random. Likewise, the blood in a person's veins won't go pouring out into the atmosphere simply because the pressure is extremely low.
Any air in your lungs will be forcibly sucked out of you. Again, this is a closed system, if you hold your breath. As long as you don't try to breathe there is nothing forcing the air from your lungs.
Your eyes will be sucked from their sockets. Thank you Total Recall (the original) for this myth. The eyes are very firmly in place. You might feel a pull on them, but they aren't going anywhere.

Absolutely none of these would happen in the vacuum of space and certainly not on the Martian surface.

Here's what will happen:

Any liquid material on the surface of your body will vaporize. All sweat, saliva (if you open your mouth), water in the mucous, and tears on the eyes, will nearly instantly vaporize. It would be quite uncomfortable, especially the eyes, but very survivable. Long term exposure to a vacuum might damage the eyes eventually, but in this scenario there are far more pressing matters.

The negative pressure may also cause your eardrums to rupture. Try to imagine the feeling your ears get on the plane at 30 thousand feet times about 100. Since you can't close your ears, plugging them with your fingers may help, but likely just postpone the inevitable pressure disparity, which will lead to at least great discomfort and possible drum rupture.

If you had the chance, you should take a deep breath before jumping out and avoid trying to breathe at all costs. Opening your lungs for a breath would very quickly draw whatever breath you had in them out into the atmosphere and also vaporize any fluid that was in them. Considering the rapid pace of this event, you would surely have permanent damage from this and begin suffocating and will die in a minute or two unless you get medical attention. There seems to be conflict in the procedure for this, with some sources suggesting that emptying your lungs would be better to avoid this. Considering the astronaut in your example is about to do a 200 meter dash he is going to need all the O2 he can get.

The cold is also a treacherous factor. At -50C the heat from your body would dissipate so rapidly that it would likely be very debilitating, perhaps causing you to seize up and clutch your extremities to your chest. It would also be excruciatingly painful. It might cause you to fall into shock. In a total vacuum however, this does not exist. A vacuum is actually very insulating, but on Mars' what little atmosphere is there is enough for you to feel the chill.

The lack of oxygen and high CO2 would be what would eventually kill you. You would eventually try to breathe and loose consciousness within a breath or two (or you might loose consciousness first then your body would try to breathe naturally). Your body would try to keep you alive as long as possible by pumping your heart faster and increasing your blood pressure, but your heart would eventually fail and you would die within seconds after that.

Evaluating your particular scenario

There are first a few things about the scenario that seem unlikely.

The astronaut would not be naked. They remain in some of their protective gear in case of emergencies like this. He would have some protection against the cold if he had to run out without it.
Certain things like extinguishers are always nearby. The idea that one was unreachable is a little silly.
Space vehicles, shuttles, and buildings all are compartmentalized like a submarine. They could simply close off the affected areas.
Fire only burns in the presence of oxygen (with few exceptions). After being closed off, compartments can be decompressed, halting the fire immediately. They can then begin refilling them with breathable atmosphere. This poses the same vacuum problem if the astronaut is in the affected area, but he won't be trying to run across the surface naked. People have survived rapid decompressions before without a single injury, as listed in my second source, however, others have never regained consciousness.
Assuming you made it to the other building, they usually only open from the inside. So unless someone saw you coming and opened the door for you, your last minutes would be better spent desperately fighting the fire until it consumed you rather than banging on the neighbor's door.

But let's say all of this breaks down and poor Astronaut Joe finds himself making a mad, streaker's dash across the Martian surface.

We should assume that our astronaut is both quite athletic and knowledgeable about the environment outside of his shelter, knowing that he should take a deep breath before heading out, but literally has no time to grab a shirt, goggles, breathing mask, or anything. Just him and Mars.

If he's lucky, it's not too cold and he doesn't seize up and fall into the fetal position within a few steps. Let's say it's -20C, which is pretty darn cold, but tolerable for a minute or two. I next see him flailing across the surface, trying to run in Mars' low gravity (no easy task). He begins to loose vision as a cloud of steam of what should be tears pours from his dry eyes. His eyelids then begin to stick to his eyeballs because there is no longer any lubrication. He is desperate to reach the other building, and his movements get more and more erratic, as his body is rapidly using all of the available oxygen. All the while, he is still holding his breath, knowing that if he attempts to breathe he will likely collapse within seconds and perish. But the more he struggles to make it, the more his innate urge to breathe overpowers his conscious thought to prevent it. Eventually, against his own willpower, he gasps and attempts to inhale deeply. He takes two or three dying breaths, if they can be called that, then falls to the ground unconscious. He dies shortly after when his heart stops and his brain tissues die.

The whole ordeal lasts under 30 seconds and he is 100 meters at most away from his shelter. If he did get lucky and actually made it to the other building, he would likely have frostbite over much of his body, permanent damage to his eyes and ears, and possibly deadly exposure to cosmic rays.

The event would be very similar to being drug by a fishing line to the bottom of the sea and drowning.

Sources:

A fun questionnaire to see how long you would last in space
What really happens in a vacuum


How does the matter that makes up the fat of your fat cells ultimately leave your body--following weight loss? I'd like to get some clarification on specifically how the matter from the fat reserves of the Adipocyte physically leaves the body.

In other words, if you were to somehow follow every atom in the fat reserves of the cells of a dieting person, then, via what hole would these atoms ultimately exit the body?

Is the answer to this question merely "exhaling through the mouth"? Or do they come out in feces too?

Note 1: This question is not to be confused with the question: "How does mass leave your body in general?" For there are several ways to accomplish this. (e.g. shedding skin cells, cutting off your arm, cutting your hair, sweating, dehydration, liposuction, bleeding, spitting, blowing your nose, etc...)

Note 2: Please see this other similar StackExchange post here:

https://physics.stackexchange.com/questions/2605/how-does-mass-leave-the-body-when-you-lose-weight

Yes, they are mostly exhaled. The carbon, hydrogen and oxygen that the fats are made of recombine to become $CO_2$ and $H_2 O$ and are exhaled.

It's the same overall chemical reaction as if the fats / carbohydrates were burnt, except it's by a different pathway, and the energy produced goes (mostly) towards driving other chemical reactions rather than becoming light and heat.


How can synonymous mutations lead to cancerous or tumorous phenotypes? After analyzing DNA sequences of an oncogene from many human cancer patients, you found that synonymous substitutions occur in a specific codon of this oncogene. Assuming that these synonymous substitutions do not exist in normal populations but do contribute to tumor development, what would be possible mechanisms that would explain how such alterations can lead to tumor phenotype?

I think you assumed that synonymous mutation means silent mutation. But this is not correct.

From Wikipedia (synonymous mutation) :

  Synonymous substitutions and mutations affecting noncoding DNA are often considered silent mutations, however this is not always the case. Synonymous mutations can affect transcription, splicing, mRNA tranport, and translation, any of which could alter phenotype, rendering the synonymous mutation non-silent

From wikipedia (Oncogene):

The proto-oncogene can become an oncogene by a relatively small modification of its original function. There are three basic methods of activation:

A mutation within a proto-oncogene, or within a regulatory region (for example the promoter region), can cause a change in the protein structure, causing

an increase in protein (enzyme) activity
a loss of regulation

An increase in the amount of a certain protein (protein concentration), caused by

an increase of protein expression (through misregulation)
an increase of protein (mRNA) stability, prolonging its existence and thus its activity in the cell
gene duplication (one type of chromosome abnormality), resulting in an increased amount of protein in the cell

A chromosomal translocation (another type of chromosome abnormality)

There are 2 different types of chromosomal translocations that can occur:

translocation events which relocate a proto-oncogene to a new chromosomal site that leads to higher expression
translocation events that lead to a fusion between a proto-oncogene and a 2nd gene (this creates a fusion protein with increased cancerous/oncogenic activity)

the expression of a constitutively active hybrid protein. This type of mutation in a dividing stem cell in the bone marrow leads to adult leukemia
Philadelphia Chromosome is an example of this type of translocation event. This chromosome was discovered in 1960 by Peter Nowell and David Hungerford, and it is a fusion of parts of DNA from chromosome 22 and chromosome 9. The broken end of chromosome 22 contains the "BCR" gene, which fuses with a fragment of chromosome 9 that contains the "ABL1" gene. When these two chromosome fragments fuse the genes also fuse creating a new gene: "BCR-ABL". This fused gene encodes for a protein that displays high protein tyrosine kinase activity (this activity is due to the "ABL1" half of the protein). The unregulated expression of this protein activates other proteins that are involved in cell cycle and cell division which can cause a cell to grow and divide uncontrollably (the cell becomes cancerous). As a result, the Philadelphia Chromosome is associated with Chronic Myelogenous Leukemia (as mentioned before) as well as other forms of Leukemia.

You might be especially interested in the second point (An increase in the amount of a certain protein)

Therefore, there is nothing impressive to find some synonymous mutations that are involved in oncogenes.


Why does the 'Positive-inside Rule' exist? Gunnar von Heijne's Positive-inside Rule seems to have been around for a couple of decades and underpins a lot of what we know about transmembrane topology. It is used to predict the topology of a given transmembrane domain, typically a helix.

My question is what are the physicochemical, or biochemical explanations for this rule? Although the literature talks about it in depth and has many examples of the rule being employed, I can't seem to find anything about the "behind the scenes" explanation.

There are not much explanations available, as far as I can see. The best explanation that I have found is that the positive charge allows the orientation of the protein in the membrane. The orientation for membrane proteins is important as a lot of them are transporters which have a dedicated transportation direction. The same is true for receptors, which transport a signal from the outside to the inside of the cell. Most of the positively charged arginine and lysine residues are found in loop regions which are located between transmembrane regions (often hydrophobic helices).

References:

Topogenic signals in integral membrane proteins.
Positive charge loading at protein termini is due to membrane protein
topology, not a translational ramp
The Positive Inside Rule Is Stronger When Followed by a Transmembrane
Helix
Membrane-protein topology


What are the implications of tigers being susceptible to SARS-CoV-2? It was recently reported that a handful of tigers and lions tested positive at the Bronx Zoo for SARS-CoV-2 (see here and here). Does this imply that the SARS-CoV-2 strain in humans mutated into a form that can infect these other species? I thought these sorts of mutations required a long time and prolonged contact between the species (which I wouldn't have thought would be present with such large cats).
Alternatively, is it possible that a single strain of the virus is capable of infecting multiple species?

A partial answer, to the question of how the virus might spread to animals I found several references

The HongKong dogs, the New York tiger, the Netherlands mink farm and the French cat have been sequenced and can be seen on nextstrain. Note the low amount of mutations in each case, which is intriguing because we expect for example that different ACE2 genes will induce some adaptation at in the viral spike. Those animals had an infection and detectable RNA in the nose for several days. For the dogs the viral load was low and in one case the sequence was identical to the owner. The minks and tiger had noticeable symptoms. A Wuhan cat partial sequence has been uploaded too, as well as a full-length French cat sequence.

A lab paper said "SARS-CoV-2 replicates poorly in dogs, pigs, chickens, and ducks, but efficiently in ferrets and cats", in particular dogs can't transmit the disease efficiently. According to them subadult cats are susceptible while adult cats are not, and the disease is upper respiratory tract.
There is a new preprint on a 4 month cat who developed severe disease, dyspnea, and had to be euthanized.

A paper found antibodies in several Hubei cats from animal shettlers and vet clinics, some of the positive cats are "stray cats", others are sick cats, and a few were cats owned by covid positive people, in those the antibodies were found to be neutralizing the virus much better than in others.

Another one found that ferrets are efficiently infected in lab and transmit the disease to each other, even if it is mainly upper respiratory tract (no severe pneumonia).

Rabbits are susceptible though less than ferrets, and asymptomatic.

Mice are not succeptible but human-ACE2 transgenic mice are and develop a mild pneumonia. Note that SARS-CoV and OC43 produced instead a deadly encephalitis.
However, through 6 ($10^{5.8}$PFU) passages into mice lungs the researchers could adapt SARS-CoV-2 through acquisition of a single mutation in the RBD allowing the virus to produce a moderate pneumonia into both young and aged mice.
The same researchers after 30 more passages obtained a super-deadly mouse adapted strain effective even at $10^2$PFU with 3 mutations in the RBD and 9 others mainly in nsp3-4-6 and N. Of note, two of the RBD mutations are in the South African variant N501Y.V2.
Something similar had been done with SARS-CoV.

The Baric lab has compared the RBD from SARS-CoV-2 and previous sarbecoviruses,
the human and mouse ACE2 protein, and through computer simulations they could find two amino acids to change in order to switch the virus from humans to mice. With 10 more passages they obtained a deadly strain in aged mice.

There are several mink farms in Netherlands where the animals got infected, this is possibly the most promising species for inter-species transmission. Edit : as predicted (first reported case) of animal to human transmission is believed to have occurred in such a mink farm. A detailed story including severe pneumonia is described in a paper.

In lab, SARS-CoV-2 is provoking a severe disease in minks as well as in Roborovski dwarf hamsters.

The Pangolin outbreak(s) : not SARS-CoV-2 but the newly discovered Pangolin-CoV in the same lineage, it killed 16 of 21 Malayan pangolins in March 2019. The virus was identified only in February 2020. The Pangolin-CoV whose RBD is very similar to SARS-CoV-2 was in this outbreak.

Cats can transmit the virus to each other. In the nose the peak was $10^{4.5}$ PFU / ml which is a medium viral load.

Similar for hamsters and macaques, the latter are used for vaccine development.
Racoon dogs show high shedding and can transmit the virus through present only minor clinical signs.
This kind of result is not surprising, most human viruses can transmit to some species and not to others, often producing a different and milder disease, which is a problem for vaccines and antibodies development.


Are some virus loads introduced to human cell but never triggered? Is there a term or any evidence of phage DNA integrating into chromosomes/ DNA but never being triggered?

For example, could a virus that affected Neanderthals still infect human cells today but is never expressed, triggered, or executed?

How often is latent viral DNA ignored by the host?

There is viral DNA within our genomes. Embedded in the genomes of all vertebrates are the proviral remnants of previous retroviral infections. It is possible that some have conferred biological benefits.
Human endogenous retroviruses (HERVs) represent the proviral phase of exogenous retroviruses that have integrated into the germ line of their host. They are transmitted vertically through the germline and are thus inherited by successive generations in a Mendelian manner.
HERVs possess a similar genomic organisation to present day exogenous retroviruses such as human immunodeficiency virus (HIV) and human T cell leukaemia virus.
Although many are defective through the accumulation of mutations, deletions, and termination signals, some HERVs have been implicated in certain autoimmune diseases and cancers and might have a role in the etiology and pathology of disease.

Within humans, the most recently active ERVs are members of the HERV-K (HML2) family. This family first integrated into the genome of the common ancestor of humans and Old World monkeys at least 30 million years ago, and it contains >12 elements that have integrated since the divergence of humans and chimpanzees, as well as at least two that are polymorphic among humans.
Here we show that the HERV-K (HML2) family has increased in copy number predominantly via reinfection, and that the family has probably retained replication-competent and infectious members for >30 million years. We also present evidence for persistent reinfection by other ERV families within the human genome, and suggest that endogenous retrovirus families are often capable of extremely long periods of smoldering infection.

Long-term reinfection of the human genome by endogenous retroviruses
The viruses in all of us: characteristics and biological significance of human endogenous retrovirus sequences
Demystified . . . Human endogenous retroviruses


What are the limitations of commercial-grade DNA genotyping compared to full sequencing? I've heard about services like 23andme, which offer genetic testing to the general public. As a person who knows very little about genetics, I'm interested in the subject and would like to know what the modern "commercial grade" genotyping really does.  What are the limitations of commercial-grade "genotyping"?  From what I've been reading, they test DNA against ~100 different markers, but do not really sequence it.

If I understand correctly, if DNA is sequenced, genetic markers and genes can be identified in it, including the newly discovered ones. However, (if I understand correctly) if DNA is genotyped, the genotyping is a one shot operation which states if some genetics markers are present in the DNA. To test against newly discovered markers, it would have to be genotyped again, right?

Thank you for any clarifications!

23andme briefly describes the technology they use here. They are testing the genotype of your DNA at roughly 1 million locations. The technology they use to do this is known as a microarray.

The limitations of using a microarray, as compared to sequencing, is that you will only find what you are looking for -- people often describe the disadvantages of microarrays as compared to sequencing with the streetlight effect/metaphor.

Arrays can only measure regions of the genome that they were designed to probe. Technically, if they probe 1,000,000 million locations, and the human genome is roughly 3.4 billion bases ... you can do the math.

In practice, SNPs tell you a bit more about just the nucleotide being interrogated, due to linkage disequilibrium (cf. tag/proxy SNPs), so the array might tell you more than you expect.

Of course, modulo sequencing errors, whole genome sequencing will tell you "everything" as far as recovering the NTs that make up your genome, but how much information that will provide you is another thing altogether (for now, that is).


How many different chains exist within a specific pdb file? More specifically, if we want to understand the different chains within a protein, is it enough to look at the fourth column of all the lines that start with "ATOM" in a pdb file, and see how many different chain identifiers exist there?

In the PDB format the lines with atoms can start either with ATOM or HETATM.

Chain ID is in column 22, i.e. it is 22nd character of a line that starts with ATOM or HETATM. (Programs that support 2-character chain IDs use columns 21-22 − it's a popular extension of the PDB format).

Yes, the number of different chain IDs is the same as the number of "chains" in the PDB file.
But note that the "chain" from the PDB format is not necessarily a real chain (polymer). It may be a bunch of water molecules or something else.


Substitute 25mM dNTPs mix with 10mM dNTPs I need to make a solution of multiple compounds, one of them is dNTPs. The recipe calls for 20 μl 25 mM dNTPs in a 1250 μL master mix. Unfortunately I do not have it available at that concentration, can I substitute 25mM dNTP mix with 10mM mix?

TECHNICAL DETAILS

$dATP: C_{10}H_{13}N_5O_{12}P_3Na_3 - MW=557.2$
$dCTP: C_9H_{13}N_3O_{13}P_3Na_3 - MW=533.1$
$dGTP: C_{10}H_{13}N_5O_{13}P_3Na_3-MW=573.2$
$dTTP: C_{10}H_{14}N_2O_{14}P_3Na_3-MW=548.1$

Would it be 50μL of 10mM dNTPs to substitute the 20μL of 25mM dNTPs?

Yes, you can do this. As long as the final mix has the proper concentrations of everything, its fine. Just make sure you compensate the by adding 30 uL (the extra volume) less of water to the master mix.


What is the name of this sea creature? I found this creature on the beach in San Diego. It is 8cm long and the end to the right is the mouth. The underside is exactly the same as what is visible. What is the name of this species.

This animal is a sea cucumber. It is probably a "sweet potato" sea cucumber (Molpadia arenicola). Here is a useful link describing this animal with pictures quite similar to yours:
https://mexican-fish.com/sweet-potato-sea-cucumber/


Trial pre-registration service that accepts non-clinical trials, or specifically ecology? I'm in the early stages of designing a trial in ecology. I'm interested in pre-registering the trial, as suggested here.

My concern is that all of the registries (that I can find) deal specifically with clinical trials, not ecological or general natural-sciences research. Does anyone know of a service that would accept pre-registration of non-clinical biological trials?

Did you try OSF.io?

They offer a free service where you can preregister trials and give them a timestamp with a DOI number etc.

I do not know if this is exactly what you are looking for, but it's the easiest solution for preregistering and I am quite sure that it would be enough to get the "preregistration" badge when you are finally ready to publish.

Here is more info on how to do it and what is essential for preregistration.


What strange jelly-like thing is shown in the photo? What is shown in the pictures below? The photo was taken at the Australia's south coast (Queenscliff). The length of the thing is no longer than 50 cm... It doesn't move and has jelly-like consistency... My guesses were either some product (egg cluster or excrement) coming out of a mollusk, a torn part of some kind of sea plant or a part of a jelly-like creature...

I agree with @Gerardo-Furtado's comment that what you most likely have here is a colonial tunicate (or sea squirt) from the genus Botrylloides.

According to images and information available via the Taxanomic Toolkit for Marine Life of Port Phillip Bay$^2$, it appears as though you have a specimen of Botrylloides perspicuus (aka B. perspicuum).

[Photo credit: Mark Norman / Museum Victoria]

[Photo credit: Mark Norman / Museum Victoria]

Background

See here for a good general description of colonial tunicates (using the example of a related Botrylloides species).

In general, colonial tunicates are composed of numerous zooids embedded in a firm matrix called a tunic (or test).

Description

B. perspicuus is a colonial ascidian that can persist in tropical and subtropical waters at depths ranging from 1-170 m.
From The Australian Ascidiacea$^1$ (my emphasis):

  External Appearance: The colonies are always robust, but very variable. Some are large, flat, stalked or sessile lobes up to about 4cm long, while others are thick, investing colonies, sometimes growing around wees or other debris. Occasionally ,the lobes are constricted along their length, and sometimes a stalked lobe grows out from a sessile cushion.

  The test is always firm, translucent and smooth....

  Zooids are sometimes in circular systems, arranged in rows along the length of the colony.

  As with other species in the subfamily, the colours of the living colony are very variable.... [including] orange zooids.

The Australian Ascidiacea$^1$ also provides remarks about similarities/differences between B. perspicuus and closely related B. leachi (mentioned in the question's comments):

One difference to note is that B. perspicuus has a firmer tunic, which might explain the retained shape of the OP's specimen even out of water.

Range

This species lives primarily around Australia, with specimens ID'd from waters off Western Australia, South Australia, Victoria , and New South Wales$^1$. The specimen is found in Port Phillip Bay$^2$, which is where the OP's location (Queenscliff) is located.

  [Source: Atlas of Living Australia]

Other Info

Another similar looking species is B. violaceus, but this species is typically found elsewhere in the world.
Like many tunicates, B. perspicuus has been known to invade non-native waters, including those of the eastern Pacific and the Caribbean.

Transport of adult colonies on boat hulls, sea chests and aquaculture equipment is the most likely cause of anthropogenic introduction.
Though ID'd as a different related species, photos showing specimens very similar looking to that of B. perspicuus were documented around the United States.

Citations

Kott, P. (1985). The Australian Ascidiacea part 1, Phlebobranchia and Stolidobranchia. Mem Qd Mus. 23: pp 278-279., available online at http://biostor.org/reference/109626/page/279
Patullo, B., 2011, Ascidian, Botrylloides perspicuum, in Taxonomic Toolkit for marine life of Port Phillip Bay, Museum Victoria, accessed 27 Feb 2017, http://portphillipmarinelife.net.au:8098/species/10656

Note: The remaining info is supported by the above linked websites without formal citations.


Why is DNA Shuffling more efficient than Point Mutation? In a related post on Biology-SE the following insightful comment was made:

  The advantage of DNA shuffling over introducing single mutations is
  that you have to screen fewer mutants and the activity/stability of
  the protein could be improved several hundred fold more.

Is there a mathematical argument as to why DNA Shuffling should be more efficient than introducing point mutations?

Even supposing each DNA Shuffling / Point Mutation step is equally "expensive"  (and in reality DNA shuffling seems much more work) they are both generating one variant per-step, right? So why is the variant in one case grossly better than the other?

Related Post: Directed evolution: Point mutation vs Insertion-Deletion vs Shuffling

You should read this paper. Here is the gist of what you are interested in:

Because most point mutations are deleterious or neutral, the random point mutation rate must be low and the accumulation of beneficial mutations and the evolution of a desired function is relatively slow in such experiments. For example, the evolution of a fucosidase from a galactosidase required five rounds of shuffling and screening before a >10-fold improvement in activity was detected4. Naturally occurring homologous sequences are pre-enriched for 'functional diversity' because deleterious variants have been selected against over billions of years of evolution...
Although shuffling of a single gene creates a library of genes that differ by only a few point mutations1, 2, 3, 4, 5, 6, the block-exchange nature of family shuffling creates chimaeras that differ in many positions. For example, in previous work a single beta-lactamase gene was shuffled for three cycles, yielding only four amino-acid mutations3, whereas a single cycle of family shuffling of the four cephalosporinases resulted in a mutant enzyme which differs by 102 amino acids from the Citrobacter enzyme, by 142 amino acids from the Enterobacter enzyme, by 181 amino acid from the Klebsiella enzyme and by 196 amino acids from the Yersinia enzyme. The increased sequence diversity of the library members obtained by family shuffling results in a 'sparse sampling' of a much greater portion of sequence space15, the theoretical collection of all possible sequences of equal length, ordered by similarity (Fig. 4). Selection from 'sparse libraries' allows rapid identification of the most promising areas within an extended sequence landscape (a multidimensional graph of sequence space versus function)


How to attain a deep conceptual grasp of key atomic/molecular/genetic/ notions? It's a total noob question, I know.

I'm a layperson trying to come to grips with basic scientific terminology. I always face a conceptual hurdle in trying to understand micro-talk. The way I'm using the expression 'micro-talk', I take it to refer to any kind of discourse that relies extensively on concepts that refer to unobservables like DNA, adenosine triphosphate, other molecules/compounds, chemical elements, atoms, etc. i.e. the kind of quasi-tangible entities that we can never perceive directly owing to our particular evolutionary history that prioritized engagement with mesoscopic objects.

Whenever I read anything in an introductory textbook, the talk of such entities is always presented as a given to me. It's not explained on how on earth we know about them (or even if such explanation is given, it's usually quite shallow and circular i.e. it makes references to the entities in question). I can recite, or rather parrot facts about them just fine. If you ask me why a second magnesium ion is important for ATP, I retort that that's because of its functional role in regulating kinase activity. I might be able to successfully make certain inferences between sentences that involve such concepts. So I might even successfully pass a scientist's Turing test, but that's all there is to it. I don't really have an understanding of what I'm talking about. I feel like I'm a robot or a medieval scribe.

How can I get over this conceptual chasm? Learning about a historical development of a particular discipline might help, but I need to find a way to systematize my study and I can't have a recourse to university right now (even if I did, I'll face the same conceptual hurdle). I have library loans and will to study, but I haven't internalized a good number of micro-talk related concepts and they feel so foreign to me.

This is quite maundering, but I couldn't put it any more succinctly. If there's anyone who experienced a similar frustrating feeling to the one I've described, I'd be very grateful if they could offer me some tips. Thanks a lot.

I'm assuming you have a reasonable high school education otherwise you probably wouldn't have posted your question.

Do a basic science course and/or read - maths, physics, chemistry, biology texts. 1st year university level should be good.

If there is anything you don't understand in these texts, go to more basic books - plus Wikipedia is good for the sciences (I wouldn´t like to read them on, say, the Arab-Israeli question), but I've never seen any egregious errors in the scientific area!

Then read Klug and Cummins "Concepts of Genetics" from cover to cover.

If there is anything you don't understand in Klug and Cummins, go back to basic texts.

I had a good background in the  sciences and then majored in Genetics with minors in Biochem, Microbiology and Immunology. I read that book from cover to cover taking notes in 3rd year (of a 4 year degree programme) and have done very well in the field.

The book covers the history of the discoveries in a very readable and approachable fashion. Obviously it is no substitute for doing a degree in the subject, but if you really wish to at least have a good understanding of the science, you could do worse than read that text!

You could also read popular science books aimed at the "interested and educated layperson" - Stephen Jay Gould, Richard Dawkins for example. Try National Geographic and even Scientific American or New Scientist. You, at least intially, will have to make a real effort, but it is very rewarding - there is nothing more fascinating than biology generally and molecular biology/genetics in particular! Best of luck on your journey!


Are efflux pumps mutations or are they originally present in N. gonorrhoea? I'll start by saying that I am no biologist. I am a math major trying to create a mathematical model for gonorrhea strain competition. My assignment is to create a model similar to a model that was already was already created, see page 9 of Evolution of within-host Antibiotic Resistance in Gonorrhea.

I wanted to try to incorporate the efflux pump into a mathematical model. Before I do that, I would first like to see whether efflux is gained through mutations. If it is, my model will be pointless since mutations are already covered in the original model from the research paper.

Feel free to add better tags. I thought mine was appropriate.

Efflux pumps are common in bacteria, as well as eukaryotes. The mutations included in their model would not include efflux pumps. A mutation could potentially affect the efficiency of a pump in a strain but the mutations in their model are not creating the pumps.


What is the exact frequency of Delta brain waves during Slow Wave NREM Sleep? I saw a TED talk about researchers playing pulsating pink noise while a test subject is in Stage 3 Non-REM / Slow Wave / Deep sleep and observing an increase in Delta wave EEG activity. This seems to indicating that the burst frequency of the pink noise is matching the dominant frequency of the Delta waves. (Skip to 5:00 to hear a sample of the sound)

My question: While a spectral analysis shows a range of brain wave frequencies, and many sources define a range such as "0.5-4 Hz", I'd like to find a more precise dominant frequency of Delta waves.

The video inspired me to write my own small computer program to make my laptop play a similar pulsating pink noise pattern on the table next to my bed last night. I arbitrarily chose 1 Hz as the pulse frequency, and the following pattern:

30 min silent (to give me time to wind down and fall asleep)
  60 min sound
33 min silent
  54 min sound
40 min silent
  45 min sound
49 min silent
  37 min sound
57 min silent
  30 min sound
30 min silent

So roughly 5x 90-minute sleep cycles with an increasing ratio of silence to noise to mimic the ratio of REM to NREM as the night progresses. I've read that REM is characterized by un-synchronized brain waves and NREM is where you see large amplitude synchronized Delta waves which the sound experiment is trying to help stimulate. Tonight I will wear my FitBit bracelet with heart rate and sleep stage tracking to see if the readings match the sound schedule.

Bonus Questions:

How credible is the hypothesis that playing sounds can affect the quality of sleep?
Would a different sound than pulsating pink noise work better?
Does the phase matter?
Also, I couldn't help but notice that Deep NREM sleep seems to be the only time you see a single large amplitude frequency dominate on EEG and it's suspiciously close to the average Resting Heart Rate of 60 bpm...are Delta waves and heart rate related?

Periklis Y. Ktonas and Atul P. Gosalia performed such an analysis. It was published in 1981 under the heading "Spectral Analysis vs. Period-Amplitude Analysis of Narrowband EEG Activity: A Comparison Based on the Sleep Delta-Frequency Band"

The bins were quite wide but their analysis showed peak power spectrum moved between 0.84 and 1.96 Hz at different times.

I think the paper would serve you well, as it highlights the difficulty in achieving what you have set out to achieve. The frequency is not constant, even over short timescales. It depends for the most part on a balance between the intrinsic, basal polarity of thalamocortical neurons, and the effect of synchronising, inhibitory input from the reticular nucleus. The latter is in turn subject to cortical feedback. There are huge numbers of neurons involved. The period between bursts, and the number of action potentials per burst, is quite variable.

Perhaps it might be possible to set up a device that alters the round in real time, based on the EEG measurement.

With regards to your 'bonus' questions:

(1) The video posted does show an effect on the thalamic rhythm, which is surprising, as it had been thought that in deep sleep, sound has no effect on the thalamocortical circuit, since it is gated at the thalamus. This shows the plausibility of the hypothesis. However, the video does not provide any evidence that this alteration in rhythm is beneficial. It is possible that it is not and this possibility should be eliminated.

(2) Clearly the sound has an effect on the rhythm, so it seems entirely plausible that there is an optimal sound to maximise the effect.

(3) It will be hard to organise the phase, given the continuous, rapid shifts in period, unless done in combination with EEG in real-time.

(4) I am not aware of any research attempting to correlate thalamic rhythms with heart beat, although it would be quite easy to do. However it is highly unlikely there is a correlation, since the thalamocortical period has a lot of variation moment to moment, whereas the heart rhythm does not. Also the thalamocortical rhythm is generaly somewhat faster.


Can someone explain this phenomena? So many parakeets sitting on a tree with no leaves ?

Parakeets are social animals that live in large groups (flocks). Under ideal environmental conditions, they can form flocks composed of thousands of birds. http://www.softschools.com/facts/animals/parakeet_facts/1274/

The fact that this tree is without leaves is irrelevant to the Parakeets. They may or may not have caused it. They chose the tree as a place to relax. It could have been any other convenient place though. If you search google images for "parakeet flock" you will see them perching on various other surfaces in a similar manner


Why don't individuals with sickle cell trait suffer from sickle cell anemia? Ostensibly, in people with sickle cell trait, half of the hemoglobin in their body would be defective.

Is it actually the case that sickle cell hemoglobin is produced in equal amounts?
If not, how is that regulated? If so, how does that still not cause anemia?

This could be a very long answer, but I'll try to keep it brief.

The first thing to understand is what causes the anaemia. I'm going to refer to defective haemoglobin found in a sickle cell patient as HbS and normal haemoglobin as HbA. Under certain circumstances (low O2 concentrations) the HbS protein is prone to aggregating into long filaments. Here is an image of a lysed erythrocyte releasing some of these filaments.

The presence of these filaments in the erythrocytes causes them to become misshapen (sickle-shaped) and this in turn causes them to get filtered out for destruction in the spleen which is continuously monitoring for defective erythrocytes (which could cause blockages in the circulation). This causes the anaemia (specifically a haemolytic anaemia, due to erythrocyte destruction, and nothing to do with a lack of iron).

The appearance of the ability to form filaments is due to a single Glu>Val mutation in the two β subunits of the haemoglobin tetramer. The new amino acid can fit into a pre-existing hydrophobic pocket on the surface of another subunit and so the molecules can daisy-chain to form the filaments.

The normal HbA can also bind on to a growing filament (it has the binding pocket) but that terminates the filament (because HbA doesn't have the Val residue). In this way people with sickle cell trait are protected from the anaemia by their normal haemoglobin.


Is oxygen's paramagnetism biologically relevant? It seems our most common everyday O2 molecule happens to be a paramagnetic one (see https://en.wikipedia.org/wiki/Oxygen).

But, does this have a biological relevance as well? In other words, Do any chemical processes occurring within the physical volume of any entity considered "living" depend in any way, shape, or form on oxygen's paramagnetic properties?

(It seems to me the answer would be "no", but I am no expert in this field!)

It sounds a bit like chem exam question to be honest... Or at least the answer does... namely that O2 being paramagnetic creates a "spin barrier" that prevents most organic compounds from reacting fast with atmospheric oxygen:

  The magnetic properties of O2 are not just a laboratory curiosity; they are absolutely crucial to the existence of life. Because Earth’s atmosphere contains 20% oxygen, all organic compounds, including those that compose our body tissues, should react rapidly with air to form H2O, CO2, and N2 in an exothermic reaction. Fortunately for us, however, this reaction is very, very slow. The reason for the unexpected stability of organic compounds in an oxygen atmosphere is that virtually all organic compounds, as well as H2O, CO2, and N2, have only paired electrons, whereas oxygen has two unpaired electrons. Thus the reaction of O2 with organic compounds to give H2O, CO2, and N2 would require that at least one of the electrons on O2 change its spin during the reaction. This would require a large input of energy, an obstacle that chemists call a spin barrier.

(quote from McQuarrie and Simon's (free) textbook Physical Chemistry: A Molecular Approach).


How are antibodies designed? Antibodies have the ability of recognising highly specific peptide sequences and bind it at their antigen-binding site.

This ability is harnessed as a tool in research to purify target structures in the cell (e.g. in chromatin immunoprecipitation, ChIP).

Now let’s say that I’ve identified an interesting target structure (such as a particular transcription factor) and I want to design an antibody to use in ChIP against said target. How would I go about producing such an antibody, taking into account that it should be both highly sensitive and specific?

I worked for a long time at a leading high-quality antibody company, so I'll try and share some of my experiences with you. The process of making a highly specific antibody (I'll focus on monoclonals) has three important parts - antigen design and immunization, cloning and subcloning, and screening/validation. Each part is crucial on its own, and the better one is performed, the higher your chances of success downstream become.

In order for an antibody to work, it needs to bind specifically to its target. I won't get into all the specifics here, as there is a good open literature on antigen design, but basically you need something that will promote a strong immune response in the host, give you a variety of clones to choose from, and be specific - it shouldn't bind other targets besides your protein of interest. There are lots of factors to consider, including antigenicity, solubility, ease of production (for immunizing and screening), steric considerations (does another protein or nucleic acid obscure the target site in vivo?), and others. Antigens can be roughly divided into two types - peptides (typically less than 20 or 30 amino acids) and proteins or protein fragments. You will most likely want to try several antigens to maximize your probability of success. After the antigen is synthesized and purified, you need to come up with an immunization schedule for priming and boosting the animal(s), then determine when and how to test them (screening), and at what time and how to harvest it for the monoclonal process.

The cloning process then comes next. Clones can be generated by a variety of methods, some widely available, such as the various hybridoma methods, and some proprietary to individual companies. My former company employed a mix of both, depending on the species of animal, using some really cool in-house tech that was constantly being improved and expanded upon. These processes are very dependent on the quality of materials being used and the expertise of the cloners. The input B cells (which make the antibodies) need to have been harvested, treated, and stored according to a set of precise steps to allow for the highest number of viable clones. Once the immortalized cells have been obtained (after fusion with the myeloma partner cells in the hybridoma process, for example) they are diluted to a pre-determined cell count and plated in 96-well plates and allowed to recover and grow for a time, during which they are secreting antibodies into the medium. This media is then tested quickly (before the cells overgrow the well), and positive wells are diluted out to (hopefully) single-cell suspensions and subcloned, or frozen down for later. The first testing is frequently by ELISA using the immunizing antigen, although depending on your application of interest it may be by high-throughput screening via flow cytometry, immunohistochemistry, or immunofluorescence. After the initial testing, subsequent steps of subcloning and re-testing can occur at a more measured pace, as the cells can be frozen indefinitely after generating sufficient quantities of antibodies in the supernatant.

This is where the quality of your screening program comes in. Your assays need to be well-designed, robust, well-documented and performed, and have appropriate positive and negative controls so that you can truly tell whether a certain clone is of interest, or performs better than an existing product. This means controlled conditions, standardized reagents and protocols, and a high degree of repeatability from assay to assay. Also, the appropriateness of your controls cannot be emphasized enough. Do you have a knockout or non-expressing sample for comparison, or a way of looking at baseline vs. induced or inhibited activity? For ChIP, unless you have a good control antibody and primer pair for your gene of interest, how will you know if the assay works? You may get a great result doing a straight immunoprecipitation-Western blot, but still not pull down DNA-bound protein. If your ChIP method doesn't produce clean DNA, you may never get binding. And if you don't have appropriate data analysis protocols in place with multiple replicate wells, you may waste time chasing noise instead of specific signal. Additionally, along with testing all your clones, you also need to titrate them to determine the optimal working concentration. I've seen a lot of antibodies that look like crap when you first test the supe, but diluted 100 or 1000X they are clean, specific, and still strong. Be patient, testing is a lot of work and requires a ton of repetition to confirm your results, but it'll be well worth it in the end.

Finally, after all this is done, you hopefully have a great clone that does what you want it to do, and better than anything else out there. You now need to decide what you're going to do with it, because if you're an academic lab and publish with it, the world will come knocking at your door. Don't slack off at the end and decide 100 ml of supernatant will be enough to last forever - save the clones and put them in a cell bank, or try to get a commercialization deal with a manufacturing company so you don't have to do all the work!

I hope this helps, please let me know if you have any additional questions or concerns.


Identification of proteins in this animation of a ribosome translating mRNA This gif is from this page
After each aminoacyl-tRNA enters the ribosome, one blue thing comes and pushes the whole tRNAs whats that? I couldn't find it anywhere.(maybe some elongation factor?)
Also it seems that some thing is transporting the tRNA itself (maybe aminoacyl tRNA synthetase?)

The protein involved in "pushing" the tRNA and mRNA is the elongation factor EF-G. The protein involved in "transporting" the tRNA is the elongation factor EF-Tu.

Quoted from the Wikipedia articles:

EF-G:

  When it binds to the ribosome A-site, EF-G causes the tRNA previously occupying that site to occupy an intermediate A/P position (bound to the A site of the small ribosomal subunit and to the P site of the large subunit), and the tRNA in the P site is shifted to a P/E hybrid state. EF-G hydrolysis of GTP causes a conformation change that forces the A/P tRNA to fully occupy the P site, the P/E tRNA to fully occupy the E site (and exit the ribosome complex), and the mRNA to shift three nucleotides down relative to the ribosome due to its association with these tRNA molecules. The GDP-bound EF-G molecule then dissociates from the complex, leaving another free A-site where the elongation cycle can start again

EF-Tu:

  The tRNA anticodon domain associates with the mRNA codon domain in the ribosomal A site. If the codon-anticodon pairing is correct, EF-Tu hydrolyzes guanosine triphosphate (GTP) into guanosine diphosphate (GDP) and inorganic phosphate. This creates a conformational change in EF-Tu that causes EF-Tu to dissociate from the tRNA of the ternary complex (and therefore leave the ribosome). The aminoacyl-tRNA then fully enters the A site, where its amino acid is brought near the P site's polypeptide and the ribosome catalyzes the covalent transfer of the polypeptide onto the amino acid . The tRNA on the P site (without peptide) moves to the E site and is then released.


What is the use of shampoo; is it for the hair or for the scalp? Apologies for the confusing question; I did not know how to better ask it.

I was doing a search on wikipedia when I found this statement.

Wikipedia's entry on hair states;

  "The hair that is visible is the hair shaft, which exhibits no
  biochemical activity and is considered "dead"."

With that being said, why does one use shampoo? Is it because of the scalp that requires nourishment and cleaning because skin is not of a "dead" nature? Or is it to maintain the silkiness and smoothness of hair? Because it seems really redundant to take care of and maintain something which is already "dead".

We shampoo our hair because of sebum. In humans, sebaceous glands are most numerous on the face and scalp, with (on the scalp at least) several glands plus a hair follicle making up a pilosebaceous unit.
Each gland secretes sebum, initially a colorless and odorless fatty substance (plus dead cells) that spreads from the scalp outward over the hair, but that breaks down by bacteria producing strong odors.
Look at a person who has not washed their hair in a week and it will be easy to understand why we wash the "dead" stuff on our heads. It looks oily and it eventually smells bad as well.


Organism-specific Kegg Pathway: Must all boxes be high-lighted/present for a reaction to occur? I'm new to using Kegg and not sure how to interpret the position of the pathway enzymes in the pathway that I'm looking at. More specifically: If all boxes (of KOs) must be present/colored green or not for a reaction to occur.

I'm looking at this pathway: http://www.kegg.jp/kegg-bin/show_pathway?ooe00010

Looking at the 'help' for Kegg indicates that the KOs represent a protein complex, because the boxes are 'stacked' against each other. Is this correct?

Specific reactions that I've been looking at: alpha-D-glucose-6P to beta-D-glucose-6P (One box is there, the other is missing).
Or the route from Glyceraldehyde-3P to pyruvate. I'm thinking that these pathways must be present, but in the very first reaction only 1 of 2 boxes are colored. I suppose it's also a possibility that Kegg's database is simply incomplete?

Your interpretation of the pathway map is incorrect.

The boxes do not represent KOs (Kegg Orthologues) and they do not represent a protein complex. They are Enzyme Commission (EC) numbers and where there is more than one box this means that there is more than one enzyme that can catalyse the reaction.

In the case you cite the two enzymes are EC 5.3.1.9, glucose-6-phosphate isomerase, as you can see by clicking the box, and EC 5.1.3.15, glucose-6-phosphate 1-epimerase. Only one is needed to catalyse the reaction.


Why is arterial pO2 normal in carbon monoxide poisoning? Arterial blood gas measurements often show that pO2 is 'normal' even though haemoglobin is bound to carbon monoxide with high affinity.

Is this because there is still oxygen bound to some subunits of the haemoglobin? Surely the CO will displace at least some oxygen, reducing the pO2? As oxygen solubility in plasma is very low, where would oxygen be in the blood if not bound to haemoglobin if there was still high  pO2?

First, let's think about what pO2 means:

pO2 is not the same as "oxygen concentration." pO2 is the partial pressure of oxygen, you can think of it as proportional to the "number of oxygen molecules per unit area leaving the solution" (or colliding with the side of the container). There is also pO2 for the atmosphere, which is going to be approximately 21% * 760mmHg = about 160 mmHg. Partial pressures are often a convenient way to measure gas concentrations, but that only works when there aren't any other interactions happening, so it's not valid for blood.

When blood comes in contact with inspired air, there are >100 mmHg of oxygen molecules hitting the solution and <100 mmHg of oxygen leaving, so there is a net diffusion of oxygen from the inspired air to the blood. If the gas in the alveoli and the blood in the lung capillaries have the same partial pressure of oxygen, there is no more net transfer of oxygen, they are at equilibrium.

Hemoglobin can't do anything to cause the blood to carry more "partial pressure" of oxygen. What hemoglobin does is to "hold on" to oxygen molecules. These "held" molecules can't leave the solution, so they don't "count" as much towards the partial pressure. Hemoglobin instead allows for a higher concentration of oxygen at the same partial pressure of oxygen. Another special thing hemoglobin does is to change its affinity for oxygen in the acidic environment of metabolically active tissue, releasing O2 at a higher partial pressure than it was initially dissolved at.

If you pumped plain saline through the lungs, it would get to about the same partial pressure of oxygen, but it wouldn't have as many oxygen molecules.

If not enough fresh air is entering the lungs, or if the air entering the lungs is low in oxygen, you would expect the blood pO2 to drop, but this isn't what happens in CO poisoning.

There is also the issue that what actually happens in CO poisoning is that affinity of hemoglobin for oxygen increases, but this is actually irrelevant to the pO2 question. The oxygen tightly bound to carboxyhemoglobin (CO-poisoned hemoglobin) doesn't "count" towards the pO2.


Co-transformation of plasmids from the same incompatibility group Can two plasmids with the same origin of replication (for example pBR322 ori) and thus from the same incompatibility group be successfully co-transformed in E. coli? What are the mechanisms that would prevent the two plasmids from co-existing together? Does it matter what is the dual resistance selection? How would the efficiency of co-transformation compare to the efficiency of a uni-transformation?

It turns out that there doesn't seem to be a specific mechanism to prevent multiple incompatible plasmids from coexisting.  Velappan et al put in more than one incompatible plasmid with different selection genes in them and put the bacteria on a single antibiotic and periodically checked for the second vector (by testing for  second antibiotic resistance).  It apparently took weeks for the second vector to disappear - many generations.

Higher copy number plasmids did better, with longer times to lose the second plasmid.  They seem to conclude that its just the natural rate of loss of plasmids that will cause the bacteria to lose the second plasmid without selection.  I imagine with two antibiotics in the culture it would take some months and you could potentially store the bacteria at -80C indefinitely.  Still in most experiments its going to be an additional headache where compatible origins of replication seem to have a more typical half life for retaining the plasmids.

They also state that the frequency of double transformations is more frequent than is usually appreciated, which seems to imply that you will get some colonies from a typical high efficiency transformation from plasmid preps.  However, they introduced the multiple plasmids by phagemid infection rather than transformation in this study.


What does "Origin" mean in NCBI GenBank? I'm having trouble determining what exactly is meant by the term "Origin" in this case. It is just before a 70 bp sequence that the page claims is a plasmid, but does not specify it to be what I assume is incomplete, seeing as I don't think there is such a thing as a 70 bp plasmid (correct me if I'm wrong). So do they mean the origin of replication to the plasmid?

Here is the page in question: https://www.ncbi.nlm.nih.gov/nuccore/M30888.1?report=genbank

The ORIGIN may be left blank, may appear as "Unreported," or may give a local pointer to the sequence start, usually involving an experimentally determined restriction cleavage site or the genetic locus (if available). This information is present only in older records.
The sequence data begin on the line immediately below ORIGIN.

[source]
Given that it's left blank in your file, it doesn't signify anything other than the end of the annotation and beginning of the raw sequence.


From a computer science perspective, how is DNA compared for various purposes? I am very interested in privacy preserving technolgies, such as Microsoft PINQ and would like to see if this is applicable to DNA comparison.

  Given that I don't have a background in biology, I would appreciate it if someone could tell me how DNA is represented in a computer (in computer science terms), and how DNA is compared in a binary format (or logical equivalent).

The privacy preserving technology I'm using allows the patient to have granular control over what DNA data they share, and how it's used. The receiving agency (medical research, FBI, fertility clinics) will receive cryptographic proof of a DNA result, without exposing all DNA values.

I suspect that each of the following use-cases focus on a certain subset of data, and if the same information was presented to all of them, it would be a breach of privacy:

Combined DNA Index System, or CODIS
State DNA index system (SDIS)
National DNA Index System (NDIS)
FBI's 13-Loci
Other government's DNA matching requirements for inclusion/exclusion
Disease susceptibility via single nucleotide polymorphism (SNP), and related heredity
Paternity tests
Evolutionary patterns

Furthermore, based on my independent research, I understand that there are many ways to determine the DNA of a given sample.  What I don't understand is if every test has the same output? (e.g. are all chromosomes are returned, vs only 23? (or less))

The value-add I am trying to provide the patient privacy, while fulfilling all legal, moral, and ethical disclosures of data requested of them.  The recipient will have assurance the data is authentic, despite the inherent double blinding of the field data.

The cryptography allows for

Redacting (or black out) certain values
Anonymously compare a numerical value, (greater than, less than, equal to) without disclosing that value.
Prove, or verifiably disprove, that a value is not in a certain list of arbitrary values.
The agency to know which DNA testing firm generated the results
The DNA testing firm to not know who the patient is, especially in cases of partial disclosure of DNA data.

Your response will help me contribute what I believe to be the moral, ethical, and socially responsible way to handling PII and DNA data.  (yes it will be open source)

From a computer science perspective, there's nothing at all special about DNA. It's stored as a simple ASCII text file consisting of repetitions of 4-15 different letters.

DNA, the molecule, is a long chain of nearly identical smaller molecules (nucleotides) joined together. The nucleotides differ only in which of four possible bases (A,C,T/U or G) they have attached. Therefore, when representing a DNA sequence, we only need to represent the bases.
There are also the so-called "ambiguity codes" which represent different possibilities:

IUPAC Code   Meaning
  A            A
  C            C
  G            G
  T/U          T
  M            A or C
  R            A or G
  W            A or T
  S            C or G
  Y            C or T
  K            G or T
  V            A or C or G
  H            A or C or T
  D            A or G or T
  B            C or G or T
  N            G or A or T or C

The vast majority of sequences, however, won't use the ambiguity codes and will only have A,C,T,G and the occasional N.

The most common DNA sequence format is FASTA, which consists of one or more sequences each of which has a header (lines beginning with a >) and 60-character long sequences. This, for example, is an excerpt of human chromosome 17:

>chr17
AAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGT
CCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTC
CCTGGGCCTGGCACCAGGGAGCTTAACAAACATCTGTCCAGCGAATACCT
GCATCCCTAGAAGTGAAGCCACCGCCCAAAGACACGCCCATGTCCAGCTT
AACCTGCATCCCTAGAAGTGAAGGCACCGCCCAAAGACACGCCCATGTCC
AGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACA
GTGcctgcgacaaagctgaatgctatcatttaaaaactccttgctggttt
gagaggcagaaaatgatatctcatagttgctttactttgcatattttAAA
ATTGTGACTTTCATGGCATAAATAATACTGGTTTATTACAGAAGCACTAG
AAAATGCATGTGGACAAAAGTTGGGATTAGGAGagagaaatgaagacata

So, in conclusion, there's nothing special about DNA. If you're writing software that compares DNA sequences, you are writing software that compares ASCII text. You can hash it, salt it and anything else you might want to do.

The only thing you should be aware of is that minor variations are very rarely meaningful. The level of identity you will need will depend on the precise biological question being asked but as a general rule, a single nucleotide difference is as likely to be a sequencing error as a real difference. You will need to collaborate with biologists in order to set up the right threshold for whatever your project is looking at.


Monozygotic vs Dizygotic heteropaternal superfecundation Update: I had a wrong assumption.

After triple checking, I now see that how ordinary monozygotic twins arise is 1 sperm and 1 ovum and then later the zygote splits up.

(1.1. and that that phil and lil from rugrats are opposite sex and identical twins is actually an extremely underrated genetic miracle, possibly giving more credibility to the rugrats theory/hypothesis. There's also semi-identical twins in a song of ice and fire - though i guess not game of thrones -, Ben 10, legend of korra, KND, baka to test, and i think samurai jack, etc)

Honest to God, what i weirdly remembered was that ordinary 'monozygotic' twins arise from 2 sperm 1 ovum and then this 'zygote' or whatever of 2 sperm and 1 ovum splits up into 2 zygotes i.e. the splitting up of the 'zygote' is a natural consequence from that 2 sperm have fertilised 1 ovum. From what I weirdly remembered, it would be natural to ask what if the 2 sperm were from different males.

(2.1. Additionally, the Phil and Lil thingy is not really a genetic miracle since all you need is a 22X sperm and a 22Y sperm to fertilise 1 ovum. Damn television. i really thought opposite sex identical twins were not that rare.)

However, apparently it is possible for 2 more sperm to fertilise 1 ovum, in a case called semi-identical twins or something, but there are apparently only 2 reported cases.

New question: Okay in the unlikely event that what would be semi-identical twins would arise from sperm from different males, well, then what?

From wiki:

Homopaternal superfecundation refers to the fertilization of two separate ova from the same father, leading to fraternal twins;6 while heteropaternal superfecundation is referred to as a form of atypical twinning where, genetically, the twins are half siblings.

There doesn't seem to be a distinction between heteropaternal superfecundation occurring with two ova and with one ovum. How will monozygotic heteropaternal superfecundation twins look like as opposed to dizygotic heteropaternal superfecundation twins and to identical twins?

Are/Were there real life cases of monozygotic heteropaternal superfecundation?

The heteropaternal superfecundation selected cases given on wikipedia seem to be for dizygotic. I tried looking up on google, but I've found so far only dizygotic.

A normal singleton child is a result of the fertilization of an ovum (with 23 chromosomes) by a sperm (with 23 chromosomes). After fertilization, the cell (with 46 chromosomes) is called a zygote.  All normal human cells (other than ova and sperm) have 46 chromosomes.
Monozygotic twins (identical twins) occur when the set of cells resulting from the early divisions of a single zygote separate into two groups.  Each of these two groups of cells proceed to form a normal embryo, with resulting (if carried to term) in twins.  Since these twins came from the same zygote, they have the same 46 chromosomes and so are essentially genetically identical.
Now how could this monozygotic process occur with two fathers being involved?  Only by having two separate sperm combine with a single ovum.  This would result in the zygote having 69 (3x23) chromosomes.  This could happen, but would be an extreme case of aneuploidy (abnormal number of chromosomes). Such a genome is massively defective due to the presence of too many gene copies, and the embryo (whether singleton or twin) will be spontaneously aborted.  Only a few kinds of aneuploidy can result in a viable fetus, almost all having only a single extra chromosome (one of the smaller ones); the most common case is having 3 copies of chromosome #21, which results in Down Syndrome.
So, monozygotic heteropaternal superfecundation has not been observed because the resulting pregnancy is very unlikely to go to term. (It's just as unlikely when the two sperm are from the same man.)


Genetic Imprinting and Cell differentiation It does not seem possible that these two processes can coexist:

1) Genetic imprinting is the phenomenon where genes are expressed differently depending on the parent of origin:

1a. Methylated stretches of DNA are not transcribed.

1b. If the gene copy originating with mom is methylated but dad's copy is not, then only dad's copy will be expressed (e.g. Prader Willi syndrome).

1c. Methylation is preserved during cell divisions.

1d. Methylation is wiped at gametogenesis, when females will erase dad's imprints and re-imprint according to maternal imprint before meiosis.

But now I'm reading about the role of epigenetics in cell differentiation, and I discover:

2) Cell differentiation occurs with lineage-specific patterns of methylation.

2a. Immediately after fertilization (prior to the first cell division), the paternal genome undergoes demethylation.

2b. The maternal genome undergoes demethylation during the first few cell divisions.

2c. Cell differentiation is accompanied and perhaps even accomplished by progressive re-methylation following these "wipes."

Source for 2): http://labs.genetics.ucla.edu/fan/papers/HuangK_RM2010.pdf
"DNA methylation in cell differentiation and reprogramming: an emerging systematic view" Huang & Fan (2010). Regen Med. 5(4):531-44.

I suspect that there is no conflict and I merely misunderstand one, the other, or both. Otherwise, how can a pattern of methylation be wiped both during gametogenesis and early embryonic stages and still be inherited?

What if imprinted regions are immune to being wiped? Also, you may be confusing DNA methylation, and histone methylation (?). Classical biochemistry posits that DNA methylation states can be transmitted from a dividing mother cell to both daughter cells because after DNA replication the two daughter chromosomes will each be hemi-methylated, and a DNA methylase that finds a hemi-methylated site will methylate the other strand (like a corrective editing mechanism).
The third thing to consider in your question is that parental imprinting is established in the germ line. In terms of wiping other epigenetic marks during early embryogenesis, the only ones present would be the ones involved in gametogenesis.  In other words, as far as we know, genes activated in muscle development are never expressed after fertilization in the zygotic cells that will give rise to the primordial germ cells, so those muscle-specific epigenetic marks don't need to be wiped off in the embryo. Neither the sperm nor the egg ever expressed muscle myosin, etc.


What concentration of hydrogen peroxide kills mold? There are numerous articles online which claim that household 3% hydrogen peroxide can kill mold growing on household surfaces, yet I haven't managed to find scientific studies that show that. My question is what concentration of hydrogen peroxide is sufficient  for killing household mold (defined usually as a reduction of 99% or some other number)?

I have tried searching online for studies regarding the efficacy of hydrogen peroxide in killing mold, and for the minimum concentration of hydrogen peroxide for killing mold, but I didn't manage to really find information on that, though I am not that skilled in finding such information and also don't have much access to scientific literature.

The CDC Guideline for Disinfection and Sterilization in Healthcare Facilities provides a good overview of various disinfectants and their effectiveness against different kinds of pathogens, along with citations if you're interested in more detail.
This document doesn't evaluate the effectiveness of Hydrogen Peroxide against Stachybotrys (black mold) specifically (the CDC specifically recommends Chlorine Bleach for this purpose), but it does describe it's effectiveness as a fungicide. Note that the level of disinfection needed to control pathogenic fungus in a healthcare setting is likely much higher than needed to control black mold in a house, but it can give you a sense of how effective Hydrogen Peroxide is overall:

A 0.5% accelerated hydrogen peroxide demonstrated bactericidal and
virucidal activity in 1 minute and mycobactericidal and fungicidal
activity in 5 minutes [656]
...
A 7% stabilized hydrogen peroxide proved to be sporicidal (6 hours of
exposure), mycobactericidal (20 minutes), fungicidal (5 minutes) at
full strength ... [655]
...
The 7% solution of hydrogen peroxide, tested after 14 days of stress
(in the form of germ-loaded carriers and respiratory therapy
equipment), was ... fungicidal (>5 log10 reduction in 20
minutes),[663]
...
A new, rapid-acting 13.4% hydrogen peroxide formulation (that is not
yet FDA-cleared) has demonstrated sporicidal, mycobactericidal,
fungicidal, and virucidal efficacy. Manufacturer data demonstrate that
this solution sterilizes in 30 minutes and provides high-level
...
Commercially available 3% hydrogen peroxide is a stable and effective disinfectant when used on inanimate surfaces
disinfection in 5 minutes [669]

From this, it seems like you'd want to use accelerated Hydrogen Peroxide, or 7% stabilize Hydrogen Peroxide to ensure fungicidal disinfection. 3% Hydrogen Peroxide is effective against bacteria, but the studies cited didn't test it against fungi.


is this true to select 100 volume higher concentration of a drug test? I am interested in knowing how to find/optimise the concentration needed for a drug effect in cell. and different organism

For example, if I use 1 micro molar for treating a cell. Should I use 10 nM when I use C.elegant ? how do you define or tune such a concentration ? Please give me reference too if there is any

Typically when working with compounds I come from two directions:

Does the drug appear in the literature and what concentration do they use?

I think a quick literature search is a wonderful thing because like many problems, often times someone else has asked your question (what's the right concentration?), and done the necessary legwork to find you a starting point. I don't think we can avoid this next part though, especially if your drug has never been used in your system/organism/etc.

Titrate your compound

For almost anything out there, even if the manufacturer has a number in mind you should always titrate for your own application. Things aren't simply going to work for you as they did for another investigator, in part, because you're never asking the same question as another investigator. A good literature search can help strengthen your finding, however.

In finding the working concentration for your compound you aren't going to be doing the optimizing. It doesn't make sense to find the best concentration when you don't know what concentration works to begin with. As a rule of thumb I try to make the range of titers broad enough that I can see where undesirable or no-effect is, so for example with a drug I'd try 100µM, 10µM, 1µM, 100nm, 10nM, 1nM, 0.1nM.

If you can pick out a good working concentration there, you can optimize by using a tighter criteria. For example, I find that 10nM works the best; now I know 100nM and 1nM are my respective maximum and minimum. May I'd try 40nM, 20nM, 10nM, 5nM, 2.5nM.

It's important to reduce technical variability by using the same starting materials such as cell number for each condition to get the best titer.


What could explain discrepancies between dates provided by the fossil record vs. the molecular clock? I am studying a mud snail genus called Ecrobia. For the Caspian species (Ecrobia grimmi), there is a discrepancy between dates provided by the fossil record and the molecular clock:

First appearance of Ecrobia grimmi in the fossil record: Middle and Upper Miocene (15.97 to 5.33 million years ago)
Age of Ecrobia grimmi as suggested by the molecular clock: 0.58 to 2.04 million years. The molecular clock was calibrated using an external marker-specific clock rate, and the climax of a geological event.

What could explain this discrepancy?

First, the example you give is unusual in that molecular dating analysis should be calibrated with fossils to set minimum ages. If Ecrobia grimmi exists in the fossil record, then no proper molecular analysis would estimate them to be younger than those fossils. There are two main causes of discrepancies between fossil and molecular dating.
For fossils you never find the oldest example of a species. If a species diverged 100 million years ago, you might not find a fossil of that lineage for millions of years, meaning that fossil estimates are almost always underestimates, but they do form a baseline upon which to calibrate molecular data. The problem with molecular data is that there is no "molecular clock". Lineages, genes and individual nucleotides all change at different rates. The best you can do is plug in fossil and/or geological dates into a model that is based on other lineages. Hopefully you have calibrated dates for closely related species, and the same genes. Even then, you do not know that the lineage you are working with will follow the same rates as the model predicts. At a minimum, you need to set a minimum possible age in BEAST to 5-16 mya.


Does the fossil record disprove Evolution? It is said by people opposed to Evolution, that the fossil record contradicts and disproves it. They say all the animals suddenly appeared, exploded everywhere, were fully formed, had no transitions, no gradualism, no change, and no sign of an evolutionary trend by which they could have emerged from an earlier type.

They then use these quotes to back this up from Evolutionists themselves:

"All the larger groups of animals, e.g. fishes, amphibians, reptiles, mammals seem to have appeared suddenly on the earth, spreading themselves, so to speak, in an explosive manner in their various shapes and forms. Nowhere is one able to observe or prove the transition of one species into another, variation only being possible within the species themselves" Evolutionist, Max Westenhofer as quoted in Dewar's More Difficulties, p. 94

"The evidence of Geology today is that species seem to come into existence suddenly and in full perfection, remain substantially unchanged during the terms of their existence, and pass away in full perfection. Other species take their place, apparently by substitution, not by transmutation" Geologist, Joseph Le Conte

"The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology (study of fossils). In any local area, a species does not arise gradually by the steady transformation of its ancestors, it appears all at once and fully formed." -- Dr. Stephen J. Gould, Prof of Geology and Paleontology, Harvard University. Mentioned in one of his regular columns in Natural History Magazine (1977) and also in The Panda's Thumb, 1980, p. 181-182

"different species usually appear and disappear from the record without showing the transitions that Darwin postulated -- we are now about 120 years after Darwin and the knowledge of the fossil record has been greatly expanded. We now have a quarter of a million fossil species but the situation hasn't changed much -- We have fewer examples of evolutionary transitions than we had in Darwins' time" Dr. David Raup, a paleontologist at the Field Museum of Natural History in Chicago. Field Museum Natural History Bulletin 50:22- 29

"Evolution requires intermediate forms between species and paleontology does not provide them" Dr. David B. Kitts, Paleontologist

"The known fossil record fails to document a single example of phyletic evolution accomplishing a major morphologic transition" Evolutionist, Dr. Steven M. Stanley

"The record certainly did not reveal gradual transformations of structure in the course of time. On the contrary, it showed that species generally remained constant throughout their history. New types or classes seemed to appear fully formed, with no sign of an evolutionary trend by which they could have emerged from an earlier type." Bowler, 'Evolution: The History of an Idea', 1984, p. 187

"We are still in the dark about the origin of most major groups of organisms. They appear in the fossil record as Athena did from the head of Zeus -- full-blown and raring to go, in contradiction to Darwin's depiction of evolution as resulting from the gradual accumulation of countless infinitesimally minute variations, which, in turn, demands that the fossil record preserve an unbroken chain of transitional forms." Jeffrey H. Schwartz, Sudden Origins: Fossils, Genes, and the Emergence of Species (New York: John Wiley & Sons, 1999)

Is this true? If not, why not? Does the fossil record prove or disprove Evolution?

Fossil records are fossil records. The people who use them to attempt to prove or disprove evolution use them to represent their causes in different ways, gleaning sometimes completely contradictory facts from the same bodies of information, sometimes even the same samples.
It is my personal belief that evolution isn't ever entirely phyletic, I like to imagine that once in a while a pup would be born or an egg would crack open and there'd be a malformed creature in there the likes of which the world has never seen, if only because its deformity has made it more adaptable or stronger to its environment, not the opposite which is usually the case with birth defects. And then yes this prototype would survive and find a mate and have offspring with its varied genes dominating, some same, some different, and begin the phyletic process.

But that's not the answer to your question. Your question isn't really answerable. Fossil records only prove that a creature once lived at that time period, and its bone structure and posture can reveal certain things to any observer, but they dont prove or disprove anything. A great deal of the works you quote speak on the topic with great finality, yet they are decades old.


How are the helices of MscL gating "attached"? I'm attempting to model the mechanosensitive channels of large conductance (MscL) in E. coli for finite element analysis purposes. I have a number of papers where this has been done, and one shows the modelling with van der Waals forces (as seems logical), but is it known how/where these forces exist?

For references, two papers I'm using have videos and pictures:
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0183822#sec013 (see the movies S1 & S2)

https://www.cell.com/action/showFullTextImages?pii=S0006-3495%2806%2971838-0

It is the combination of intra- and inter-molecular interactions that determines the conformation of the protein.

There are two types of interactions: bonded and non-bonded. There are two types of non-bonded interactions: electrostatic and non-electrostatic. Electrostatic (also known as 'polar') interactions are usually modeled using Coulombic potential energy equation; non-electrostatic (also known as 'non-polar' or 'van der Waals') interactions are usually modeled using Lennard-Jones potential energy equation.


Strange Striped Insect identification (Northern Indiana) These bugs are coming out of some wood that I cut and burned in Northern Indiana (USA) . I am not sure if it is coming out of a white ash, cherry or oak.  We did have the emerald ash boarer come though the area -- is this an ash boarer?

Thanks.

This is actually a Painted hickory borer (Megacyllene caryae).

According to the Virginia Cooperative Extension (and here), this species is frequently misidentified as a Locust Borer beetle (Megacyllene robiniae).

Here are their pictures side-by-side (M. robiniae on the left and M. caryae on the right):

Pretty similar, right? There are some differences though:

Appearance:

M. robiniae description (from Virginia Cooperative Extension):

  Both males and females have black bodies with bright yellow markings. These markings are most notable in the "W" on the first pair of wings.  Legs are red and antennae are black. These long antennae place it among the "long-horned" beetles.

The distinction for M. caryae is the white 'W' stripe. From OSU Extension:

  The first marking from front-to-back on the elytra is also a yellow horizontal band; however, the second marking appears as a distinct "W" that is light yellow to cream-colored.

The following image from the Ohio State Extension better demonstrates the white W markings of M. caryae (similar to the OP's picture):

These two insects also differ in Behavior ( this is important).

From OSU Extension:

  Painted hickory borers emerge from cut wood in the spring and locust borers emerge from live trees in late summer to early fall.

Since the OP found this in the spring coming from firewood, it further points to the painted hickory borer.

Finally, they differ in the species they infest:

From the Virginia Cooperative Extension:

  The locust borer is a native insect that attacks black locust (Robinia pseudoacacia L.) and its ornamental cultivars... Unlike locust borer adults, painted hickory borer adults...attack stressed or recently cut hickory and other hardwoods.

M. caryae is named for it's preferred wood, the hickories (Carya spp.).

According to OSU Extension, M. caryae also commonly infests the recently dead wood of ash, black locust, hackberry, honeylocust, oak, Osage orange, walnut, and butternut trees.

M. robiniae, on the other hand, gets it name from the larvae living in and eating their typical host tree, black locust (Robinia pseudoacacia). Adults are also often found eating goldenrod species.

Should you be concerned? Not according to the OSU Extension page:

  Fortunately, painted hickory borers only infest dead wood that has been cut for less than one year. ... The beetles will not infest older dead wood; they will not infest wood that has been dried or processed into home furnishings, or used as structural wood.  So, beetles that emerge from infested firewood in or around a home are only a nuisance pest.

A quick search for M. caryae turns up few other sources, but you can find additional fact sheets for M. robiniae here, here, and here.

For those that don't know trees: here is a link to learn more about the common North America hickory species, and below are some images of common hickory species. More info about black locust (Robinia pseudoacacia) can be found here.


Why do people cut back on kilo-calories? I am learning about specific heat in science and I learned about how the specific heat for water is called a calorie, but that is different to what is on the food label.
On the food label, that calorie is actually a kilo-calorie. My teacher went on to explain that if somebody handed you a bowl of ice-cream that contained 500 Calories (i.e. Kilo-Calories) then, that was enough to raise 500kg of water 1°C.
If a kilo-calorie is just raising your body temperature, why do we cut back on calories?? What effect does a kilo-calorie have on your body other than raising your temperature?

P.S. How can we burn calories?? This seems, at least to me, like an abstract thing... burning heat....

The calorie is a unit of energy. Our body uses the energy found in food to create ATP (a molecule that is handy to deal with energy) with the help of oxygen (that we breath in). ATP can then be used for plenty of tasks such as importing ions through a cellular membrane or more ultimately walking, talking, warming up your body, etc...

Saying that some food contain 100 calories (not kilo-calories) does not mean that it will heat up 100 grammes of our body water by one degree (Celsius). It only means that we are ingested the same amount of energy than the one that is needed for warming up 100 grammes of water by 1 degree (Celsius).

You might to have a look at CrashCourse video on ATP and respiration.


Plotting metabolic networks? I need to draw a map of the core metabolism of E.coli. Associated with each reaction in the map I have a number that indicates the flux through this reaction. I want the map to reflect these fluxes through the color of each reaction in the map.

I have tried using tools like Mathematica and Cytoscape, but it is very hard to get a nice layout of the metabolic network. I have seen maps of E.coli metabolism which look very nice on paper. What I need is a map like these, but where I can define the colors of the reactions.

For example, see the image below for an example. Forget about the yellow bounding boxes delimiting compartments. I can spare those.

I'm not sure if they will be useful for your application, but you should look into software used to visualize ecological networks (and maybe also software used for drawing electrical charts). The type of data used there is very similar to what you want to plot, with nodes and links along with metadata for links on e.g. rates or connection strenghts.

I can point you to mangal by ecologist Tim Poisot (blogpost on mangal here), SBGN (Systems Biology Graphical Notation), and there is also the R-package diagram. However, I haven't used them much so I cannot say how useful they will be.


In which month should I map maritime vegetation? I'm studying habitat use by Brent Goose in the UK, a species that feeds on maritime vegetation. It's main food types are Zostera sp., Ruppia sp., Ulva / Enteromorpha sp. and Puccinellia sp. I plan to map these vegetation types on an inter-tidal mudflat in North-east England during the summer.

I want to choose a month to map these vegetation types that will allow the most accurate mapping of their distribution of vegetation across the mudflat. I think there are two considerations 1. the month they easiest to identify 2. the month they are most visible.

Which month should I choose?

One way to approach this problem would be to look at herbarium collections of the taxa that you're interested in. Usually, a flowering or fruiting specimen is easiest to identify; but no matter what character is best for your taxon, if you look at the herbarium collections and see that
-most of the collections identified to species, or
-the especially good-looking collections, or
-flowering/fruiting collections,
were made in a certain month or season, that could help you to narrow down your time window.

As a bonus, in reviewing herbarium collections, you'll have given yourself a step towards being able to identify the species.

Some herbaria have some collections online; here, for instance, are records and images for online Puccinellia collections at a number of UK herbaria.


Body's response to second dengue attack I have read in wikipedia that the first dengue virus infection is cleared by the body very easily. The second infection, however, is dangerous. How does body fight second infection, or does it has any tool to fight it given earlier antibody will be ineffective?

From the Wiki page for Dengue fever, I believe the text you're referring to is:

  ... those who have previously been infected with other serotypes of dengue virus ("secondary infection") are at an increased risk.

Notice that the text says, "...infected with other serotypes of dengue fever ...". That being said, your focus should be on the effects of reoccurring infections brought about by different forms of dengue fever.

In 2011, the School of Public Health at University of Berekeley published a study that addressed this very situation. According to the article:

  In two clinical studies of dengue in Managua, Nicaragua, we observed an abrupt increase in disease severity across several epidemic seasons of dengue virus serotype 2 (DENV-2) transmission. Waning DENV-1 immunity appeared to increase the risk of severe disease in subsequent DENV-2 infections after a period of cross-protection. The increase in severity coincided with replacement of the Asian/American DENV-2 NI-1 clade with a new virus clade, NI-2B.

And to quote lead author Molly OhAinle, which I believe answers your question:

  With the second infection, the antibodies sort of recognize the new type of viruses, but not well enough to clear them from the system ...  Instead of neutralizing the viruses, the antibodies bind to them in a way that actually helps them invade the immune system’s other cells and spread.

So, given that the immune system represents all behaviors within our body that defend against foreign bodies considered to be a threat, if the immune system itself is helping the virus, then no, there is no other line of defense against  the infection (excluding treatment intervention).

Lastly, here's an image from that publication, showing the seasonal patterns of dengue fever with respect to the various serotypes:

For finer details, you can access (and download) the publication for free; you just need to create an account on this site.