human biology - What causes sinus pain and congestion?

Inflamed sinuses are often associated with some kind of illness or irritant such as flu, the common cold, or hay-fever. As an example the cold causes sinus pain and inflammation because the virus is attacking/located in the nasal passages which causes swelling in the mucus membrane (the mucus membrane lines the sinus cavities). The swelling, along with increased mucus production, combines to create clogging and the pressure associated causes pain. Humidity will help loosen the mucus and anti-inflammatory medication should help reduce pain by reducing the mucus build up and swelling - thus relieving pressure.

The increase in mucus production is because of the role it plays in our bodies - it is produced to trap foreign bodies and help keep our system clean. The more mucus we produce the more our bodies are trying to clean up. This can cause an excess which is difficult to clear such that our sinuses become blocked and dried mucus becomes an irritant.

Sinusitis is the painful condition of swelling in the mucus membrane. Sinus comes from the latin for bent or curved surface, and -itis is from greek meaning swelling or inflammation linked to disease.

In summary: Painful sinuses, aka sinusitis, are painful because of infection in the mucus membrane producing swelling and excessive mucus build-up.

physiology - Why do bats huddle during late fall?

This is basically a trick question and a bit of a cheap shot. All of the reasons cited boil down to "bats huddle to conserve heat", they are basically the same, single, reason.

In order for bats to feed, they need to move, fly out of their cave or wherever they happen to sleep and go forth and look for food. Therefore, they will not be able to huddle while feeding because they will be flying around trying to find fruit or donkeys or whatever each species feeds on. Unless they can figure out a way to huddle while flying, they will not be able to huddle while feeding and so number 5 is wrong.

virology - Why are some viruses not communicable person-to-person?

Below are two quotes from the CDC about Hantavirus:

"Researchers believe that people may be able to get the virus if they
touch something that has been contaminated with rodent urine,
droppings, or saliva, and then touch their nose or mouth."

and:

"You cannot get the virus from touching or kissing a person who has HPS."

This is hard to believe. So, since human saliva is not a problem, can you be contaminated
by human urine or human droppings? The only way for me to interpret this logically is to
say that this virus lives at the end of the digestive tract (for both rodents and humans)
and people can be kissed because they have much better hygiene than rodents. Is there a
better interpretation?

Also, is there a simple reason why Hantavirus leaves the mouth (moving to the end of the
digestive tract) of an infected animal, but influenza does not?

evolution - Why is venom more common in fish and snakes than other vertebrates?

This write up by Carl Zimmer basically covers anything I could have said. He links to a number of resources, in particular this pdf, which at a cursory glance looks utterly fascinating and very well done. Figure 1 in that pdf sums it all up, I guess, or to quote Carl:

"Each lineage of venomous animals became deadly on its own, independent of all the others. And yet, in the end, their venoms echo each other... These results show that there are a limited number of ways to kill your victim quickly. No matter what genes you borrow for the evolution of venom, they will end up very similar to other venoms."

Another Zimmer piece specifically points out research purporting to show that snake venom genes are much older than snakes, maybe 200 million years old. That gets around but doesn't quite answer your question. An older review tried to coalesce things (as best as he could in '92), spending time focusing on insectivora and dealing with mammals. The theory is that while venom is an excellent advantage, it requires a significant investment and is often slow-working. In a world with sharp teeth capable of tearing, venom may not be necessary. Mammals, for example, might evolve to not use venom, as it may not be suitable for their high daily energy demands. The pdf linked above briefly touches on the concept of "reverse recruitment," where venom genes may be usefully re-purposed for other biological processes.

human biology - Do teeth have the capacity to heal?

Yes, it can be done to a certain degree.

Cementum is capable of repairing itself to a limited degree and is not resorbed under normal conditions. Some root resorption of the apical portion of the root may occur, however, if orthodontic pressures are excessive and movement is too fast. Some experts also agree on a third type of cementum, afibrillar cementum, which sometimes extends onto the enamel of the tooth.

Cementum is produced by cells called cementoblasts.

more here:
http://en.wikipedia.org/wiki/Cementum

bioinformatics - Models of quorum sensing for multi-agent systems

Quorum sensing is a system of stimulus and responses correlated to population density that is used by bacteria to coordinate gene-expression. I am looking for a simple computational/mathematical model of quorum sensing that abstracts away from the details of the mechanism implementing it inside the agent, but keeps the key inter-agent properties like diffusion rate, range, and timing.

Is there a standard abstract mathematical model of quorum sensing used by biologists?

I am not interested in the particulars of a specific organism, but would like a general model I could apply to capture the 'gist' for any organism that relies on quorum sensing for part of its behavior.

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Bernardini et al. (2007) provided an extension to P-systems incorporating the basics of quorum sensing, and Romero-Campero & Pérez-Jiménez (2008) have used their approach to model bioluminosity in vibrio fischeri. This approach is conceptually appealing to me, but that is because I am predominantly a computer scientists. Although P-system can be used for modeling biological systems (Ardelean & Cavaliere, 2003), they still feel fundamentally computer-science-y and are typically not published in orthodox biological venues. This makes me suspect there is a more standard approach among biologists, probably via dynamic systems and diffusion equations.

pharmacology - Why is Paracetamol so great?

Paracetamol is a pain killer, it does not treat the cause of your illness, it only alleviates the symptoms. From its wikipedia page:

Paracetamol [...], chemically named
N-acetyl-p-aminophenol, is a widely used over-the-counter analgesic
(pain reliever) and antipyretic (fever reducer).

So, paracetamol does not make you better. Your immune system makes you better. Paracetamol just makes you feel better while you are waiting for your immune system to get an infection under control.

You should be aware that it is only safe in small doses and a toxic dose is not that much more than the recommended one (source):

Risk of severe liver damage (ie a peak ALT more than 1000 IU/L)

Based on the dose of paracetamol ingested (mg/kg body weight):

Less than 150 mg/kg - unlikely
More than 250 mg/kg - likely
More than 12 g total - potentially fatal

Again from wikipedia:

While generally safe for use at recommended doses (1,000 mg per single
dose and up to 4,000 mg per day for adults),[6] acute overdoses of
paracetamol can cause potentially fatal liver damage and, in rare
individuals, a normal dose can do the same; the risk may be heightened
by chronic alcohol abuse, though it is lessened by contemporary
alcohol consumption. Paracetamol toxicity is the foremost cause of
acute liver failure in the Western world, and accounts for most drug
overdoses in the United States, the United Kingdom, Australia and New
Zealand.

I am sure someone else can explain the pharmacokinetics and details of action of paracetamol. I just wanted to point out that paracetamol can be dangerous and should be treated with respect.

genetics - Difference between mutation and DNA damage

Have you read the DNA repair article on Wikipedia? The DNA damage and mutation section answers exactly what you're asking:

DNA damages and mutation are fundamentally different. Damages are physical abnormalities in the DNA... [and] can be recognized by enzymes, and, thus, they can be correctly repaired if redundant information, such as the undamaged sequence in the complementary DNA strand or in a homologous chromosome, is available for copying.... In contrast to DNA damage, a mutation is a change in the base sequence of the DNA. A mutation cannot be recognized by enzymes once the base change is present in both DNA strands, and, thus, a mutation cannot be repaired.

Here's the entry from the NCBI MeSH Glossary saying the same thing:

Injuries to DNA that introduce deviations from its normal, intact structure and which may, if left unrepaired, result in a MUTATION or a block of DNA REPLICATION... They include the introduction of illegitimate bases during replication or by deamination or other modification of bases; the loss of a base from the DNA backbone leaving an abasic site; single-strand breaks; double strand breaks; and intrastrand (PYRIMIDINE DIMERS) or interstrand crosslinking. Damage can often be repaired (DNA REPAIR).

And for mutation:

Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.

genetics - How diverse are dogs in their traits other than appearance?

I've asked this question about dogs not so long ago, and the short answer was - dogs are the most diverse looking species of mammals because they got a small number of genes that have a big impact on appearance.

I would like to ask a follow up question- differences in appearance are easy to notice, and I would like to learn about other traits that might be genetically based.

Are there other major differences between dog breeds, like longevity, cognitive performance, friendliness, etc? Or are all dogs more or less the same in traits other than appearance?

Are there plots of traits like these among different dog breeds that identify outliers?

biochemistry - Can the sulphur content of biological material be reliably calculated from fat, fibre and protein contents (Weender Analysis)?

I would say theoretically yes, if you know lots of other information, but practically no, because of all the unknowns.

According to this paper cysteine content and therefore sulfur content of proteins vary depending on what kind of organism your organic material is coming from. Animals have more, bacteria tend to have less.

The sulfur content as a fraction of protein content in a given animal or plant is constant or nearly constant across the entire animal/plant. If a sample's protein content is 50:50 corn protein:sheep protein it's possible to estimate the sulfur content of the protein fraction from the sulfur contents of the sources of the protein.

In addition the sulfur content can be affected by fermentation and sulfur/sulfate-reducing bacteria, many but not all of which are anaerobes. So figures for whatever the source of the feedstock is (as far as cysteine content) can be affected by whatever happens to it afterwards. Chicken waste with a high sulfur content allowed to ferment may give off fairly large amounts of hydrogen sulfide, lowing the sulfur content without necessarily affecting the bulk protein content. The reverse might also happen, where protein is digested and sulfur is released as sulfates but kept in the mixture.

Even if you know for certain the sources of all of the protein(and that no further biological activity has changed them), the unknown amount of organic acids is going to throw off your sulfur estimates if there are sulfur-containing organic acids in the N-free fraction.

genetics - Does DNA contain information beyond protein synthesis?

What a timely question.

Does DNA contain information beyond protein synthesis?

Yes. In fact, protein-coding genes only constitute a tiny part – less than 2% – of the whole DNA. There are of course many other genes which aren’t protein coding: there are genes for ribosomal RNA and we find more and more genes which code for small RNAs, such as tRNA. But even if we count all those genes we won’t come above maybe 10% of the total DNA.

Most of the DNA is instead devoted to the regulation of gene expression, most importantly via the binding of transcription factors (but the picture is much more complex than that). With the conclusion of the ENCODE project, a whole slew of papers were published which show that in fact most of the DNA is actively implicated in the binding of various factors (although it’s not known how much of that actually contributed to the cell’s fitness).

But I’ve hijacked your question a bit here. So let’s come back to what you’re actually interested in:

What about higher levels, such as organelles, cells, tissue, organs?

There is no known mechanism (beyond the already mentioned regulation) which would encode such information in the DNA. Excluding its existence categorically may be hard but given that we haven’t found any machinery which would be necessary to read such information, we can be pretty confident that it doesn’t exist.

If not, what guides those levels of structure?

The higher levels of organisation are to all appearances emergent. That is, they are a consequence of the lower level organisation. For instance, take the cytoskeleton which carries much of the cell’s physical structure. It is composed of different protein complexes which form spontaneously through assembly of globular proteins (such as actin). The are several ways in which the process can be guided but strikingly it’s largely stochastic – i.e. mostly unguided, and it still succeeds in building a stable skeleton, simply by virtue of molecular properties encoded in the proteins.

I think this is a common theme of cell organisation: the elementary building blocks are encoded by the DNA, and their abundance is tightly regulated. Everything else, i.e. higher-level organisation – follows from that: abundance and localisation of the right proteins.

As for differentation into different types of cells, and organization into tissue and organs: the information and control systems for that are currently unknown.

In fact, much is known here, and it goes back to regulation on the level of DNA: we know that genes are differentially expressed depending on the cell type and stage of development (and the stage in the cell cycle). This regulation is highly complex and decoding it is a slow process. Nevertheless, the factors involved here are decoded one by one. This is the domain of developmental biology.

Protocol for measuring stamina of arthritic mice

I believe the standard is an graded-speed treadmill test. An example pub:

Genetic variability in forced and voluntary endurance exercise performance in seven inbred mouse strains

If there is a particular ethical concern, you should always have your institutional review panel review it. If you call up your department of animal resources (or what ever it is called in your institution) they will almost always give lists of preferred LOPs.

Another option would be to score time sleeping if you have them under behavioral surveillance. The problem with this is the large amount of man hours needed, even watching tapes at high speed. Instead I recommend you check this paper out:

Evaluation of two automated metrics for analyzing partner preference tests

Then to get accurate scoring, I would put a strongly colored bedding pad in a corner so the computer could pick it up. Be sure to put the bedding in at least a week before so the mice get used to it and actually sleep on it.

vision - What gives things their colour?

I do not know how to explain to a 6 year old how we are able to perceive colour. Does anyone know how this can be explained?

Well, depending on the depth you want to introduce her to, it can be difficult to explain to adults - much less children. You explained the basics well enough. Without going to the molecular mechanisms, here's a useful diagram:

Light will pass through the eye and Retina until it hits the Cones and Rods. That produces a reaction (which I'll address next) - which then causes signals to either resume or cease (Rods are, ironically, shut off by light - not turned on). These signals pass through Ganglion cells, through the Optic Nerve, and interpreted by the brain. When some cells are switched on, like a 3-Way traffic stop, they will prevent the information from other cells being transmitted.

A simple way of explaining it might be that inside our eyes are millions of teeny-tiny molecules that act like light-switches, and the brightness and color of light determine which of the "light-switches" are on or off.

If you want to go further into the actual mechanisms (or just have the background knowledge for future reference) the next diagram shows the mechanism itself (and the original in full-size since the one shown is squished if you prefer):

The big things to note above is the change from cis-Retinal to trans-Retinal which occurs after a Photon is absorbed. This causes signaling molecules to go a bit wild, open ion channels, and the depolarization of the membrane propagates the charge down the cell - much like a neuron.

I have never quite understood this idea that an object has a colour depending on the light that hits it. Okay, I understand that in low light objects have a different colour because there is a not much light hitting it and that different objects absorb different wavelengths of light and therefore appear as different colours.

Well, let me stop you here. Low-light is a different situation than colored-light. Let's get the basics down:

Photons are absorbed by the electrons of the atoms that compose the molecules of an object. Whatever Wavelength of light is not absorbed by the electrons is reflected, and it's this Wavelength that we perceive as the color of the object as our Cones absorb the reflected light.

Photons can also be emitted when an electron moves to a lower-energy state. The Wavelength emitted by the electron is directly related to the difference between the High and Low energy states, as this diagram shows fairly well:

The emitted photons are the object's "Incandescence" - which is when an object produces a color of light by itself. The color you perceive is NOT going to change if the object emits incandescent light because the object is generating its own light. Neon signs are a great example: The gases being subjected to a current emit light, and will appear whatever color it's supposed to be whether or not it's a blue moon or sunset.

Photons which are reflected and not emitted - i.e. almost everything that doesn't have a power source - as I said above, are then absorbed by our Cones and our brain interprets the signals to produce a color.

The reason why objects that reflect light can change color is because not all environmental light is the same. Red objects will appear Black under Blue light because Blue light doesn't contain Red Wavelengths - there's nothing to reflect, so the object absorbs all of the available Wavelengths - the very definition of Black!

A lot of our color perception depends on ambient light, and most of the time - thanks to the Sun - that is a full-spectrum white light. Which brings me to answer the last bit of your question:

What I don't understand is that if I place a bar of gold a bar of silver side by side in the same lighting conditions they do have different colours, so therefore there must be something inherent in these object that give them different colours. What is that something?

Yes, there definitely is something inherent in both objects. That is: Their electron configurations absorb different chunks of the spectrum, and accordingly reflect different chunks of the spectrum. Although that's still a bit simplistic, since metals have some unique properties that other Elements do not. Their electrons exist in more of an "ocean" than around central atoms, but that's a whole other question.

As a fun bit of Trivia to impress your daughter when she's old enough, it's always a fun fact to know that the color Yellow is completely constructed in your head.

The human eye only has Rho (Red), Gamma (Green), and Beta (Blue) color receptors which have the following absorption pattern (from photo.net):

What everybody sees as "Yellow" is actually when both the Green and Red receptors are activated at the Wavelength where they intercept above, which your brain interprets as "Yellow":

Because your brain does a lot of processing, despite having only three color receptors we can perceive millions of colors (and shades/tones). Now for a while everywhere you look you'll be utterly amazed at what's going on, and you rightfully should be. ;-)

How many people are required to maintain genetic diversity?

Inbreeding isn't negative at all, so one couple would suffice for colonization.

Inbreeding fixes recessive traits and the ones displaying unwanted traits can be culled. Actually, inbreeding is one of the most potent weapons of evolution, it speeds things up greatly. We went through a major bottleneck event ourselves and lived to tell the tale.

The exact number of individuals needed for a healthy species that will survive X number of generations depends on the species though. To maintain healthy genetic diversity and establish enough different alleles to allow for sustainability of the species. I don't remember the exact number but I think for humans it was something between 1000 or 10000, and if you get below that number the species will likely go extinct by natural causes.

Of course, everything is completely different when you have full control over who mates with who. But still, in the above example of 1 couple, they can successfully start a seemingly healthy population, but due to low genetic diversity they - as a species - won't be able to respond to, say, increased radiation, changes in atmosphere, a virus, bacteria, shortage of food, etc. That's why 1 couple is basically enough, but to ensure longetivity of the species 25 couples is far from enough.

genetics - Why Can't A Male Mule Have Offspring?

It's essentially genetic. The mule is a hybrid of a male donkey and female horse. A donkey has 62 chromosomes, a horse has 64 chromosomes, and a mule has 63 (mix of 62 and 64). There is a mismatch between both number and structure of the chromosomes and as a result, most mules are infertile.

human biology - What controls the breast size?

The known factors seem to be mainly oestrogen and genetic (although I haven't been able whatsoever to find detail on what genes):

Manning et al (1997): Breast asymmetry and phenotypic quality in women. Evolution and Human Behavior, 17 (2): 129–143. (http://www.sciencedirect.com/science/article/pii/S0162309597000020)

Our data support the thesis that mammotropic hormones, particularly estrogen, are harmful because they suppress the immune system. Heavy women with high levels of body fat produce more estrogen and, therefore, bigger breasts. However, more estrogen leads to an increase in breast asymmetry. Women with “good genes” are able to produce symmetric breasts despite the presence of large quantities of estrogen. Large and symmetric breasts are therefore honest signals of high phenotypic quality in women.

bioinformatics - Deterministic model of lambda-phage lysis/lysogeny [MATLAB]

For homework questions, the policy is to see some work from the poster. Since you don't know programming, I've outlined what the code is doing, beyond the simple operations (+, -, /, *, ^), to get you started. I think you should be able to implement the models with this information, and I'd be happy to confirm your own answers.

---

So the best way to figure out what any line of code means, in any language, is to type it and see what happens. To help you get started with programming in MATLAB:

Any text following a % (on the same line) is a comment: it does nothing in the program, and is only there for you to write notes to yourself.

The first two sections, Time-Related Constants and Simulation Constants, are just setting variables. It's like saying x = 3, so that later on you can do other operations with x.

The semicolon at the end of a line (in MATLAB) suppresses the output of the line. See what happens if you type x = 3; versus x = 3 at the command prompt.

In iteration constants, length is just a function that tells you the length of the vector. X_rna_0 was previously initialized to go from 0 to 1.4 in steps of 0.2: the syntax is vector_name = start:step:end.

The simulation variables section is creating xyz-matrices, with all values initialized to zero. The length in x is xr_max, and so on. The idea is that, later on, at each step in Euler's method and each value of xr_max and xp_max, you'll save the value of X_rna.

The initial conditions are being set using meshgrid, which is best explained here. The : means all of the rows/columns, corresponding to position: say you had a 3 x 3 matrix called apple. apple[:,1] gives you all the first column (1) of all three rows. apple[1,:] gives you the first row (1) of all three columns. The .' means that the matrix is being transposed: again, the best way to see what's going on is to create a matrix of your own, perform the operation, and see if what you get is what you thought it would be.

For loops, you can read about here, for a start. I do not think understanding this loop requires more information than that page.

Dot before ^2 means that each element of the matrix is being squared; you are not multiplying the matrix by itself.

That should decipher most of the code for you. If you have further questions, feel free to comment here.

EDIT: Question 2 asks you to make a plot. A plot of y vs. x would be made by typing plot(x,y)

Also, help on a particular MATLAB function can be accessed by typing help name_of_function.

human biology - How does fever physically work?

What is the physical mechanism that causes temperature to rise during a fever? I know that somehow the hypothalamus "orders" to increase the standard body temperature regulation, and this should stimulate mitochondria to produce more ATP. Is that right?

Is this the only heating physical mechanism (through increasing production of ATP) that acts during a fever?

entomology - Why do cockroaches flip over when they die?

It is a result from the insecticide you are using. From this excerpt from the 10th Edition of the Mallis Handbook on Pest Control:

Neurotoxic insecticides cause tremors and muscle spasms, flipping the cockroach on its back. A healthy cockroach can easily right itself, but without muscle coordination, the cockroach dies on its back. Cockroaches exposed to slow-acting insecticides that target respiration (energy production) also can die “face-down,” as they run out of energy without experiencing muscle spasms.

Here's also a website from UMass describing it in more detail:

Most of these insecticides are organophosphate nerve poisons. The nerve poison often inhibits cholinesterase, an enzyme that breaks down acetyl choline (ACh), a neurotransmitter. With extra ACh in the nervous system, the cockroach has muscular spasms which often result in the cockroach flipping on its back. Without muscular coordination the cockroach cannot right itself and eventually dies in its upside down-position.

And an entomology professor even answered this for Maxim:

Most insecticides are poisons that target a bug’s nervous system. When you spray a roach, those neurotoxins cause tremors and muscle spasms, which flip
it onto its back, and without muscle coordination, that’s the position it dies in

death - How long can a naked human survive on Mars?

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:

1. 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.


2. 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.


3. 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.


4. 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.

1. 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.


2. Certain things like extinguishers are always nearby. The idea that one was unreachable is a little silly.


3. Space vehicles, shuttles, and buildings all are compartmentalized like a submarine. They could simply close off the affected areas.


4. 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.


5. 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