genetics - What makes a gene dominant or recessive

Generally if one of the genes' biochemical functions becomes knocked out completely, the other copy will fill in for it, making the trait recessive - requiring both copies being knocked out.

An example of such a recessive trait is Albinism - if both copies of the enzyme participating in melanin biosynthesis are ineffective, the result is someone with no pigment.

Dominant genes are often variant genes which convey a new ability (phenotype) and as such the trait can show up with just one copy has this variant. Phenylthiocarbamide tasting is an example of this dominance. If both copies of the gene were the variant, the original ability might disappear - making the original trait dominant as well. On the molecular level, genes most often encode proteins which perform some function for the cell: For example, they could be enzymes and catalyze chemical reactions. They could also have some structural function, such as make up the "muscle" part of your muscle cells... You get the idea.

In the most simple case, the dominant allele encodes a protein that can perform its function. For example, the dominant allele for the CFTR gene encodes a channel that can let chloride into and out of the cells. The recessive allele, on the other hand encodes a protein that cannot do its job correctly (this also called a loss-of-function mutation). So if you inherit a functional copy from one parent and a non-functional copy from the other parent, you will still have one copy of the protein that can do its job. Only if you get a nonfunctional copy from both parents will you have a recessive condition called cystic fybrosis.

microbiology - If a human takes antibiotics are all bacteria in the body killed?

No

There are several reasons why this might not be true, as Alexander has discussed. An antibiotic often has a molecular target that isn't present in all bacteria, it's extremely hard to get antibiotics to certain parts of your body, and some bacteria will be defended against a antibiotic attack by biofilms, resistance mechanisms, and sheer statistical probability.

That is not to say that many don't die. Indeed, one of the major causes of Clostridium difficile infection is that antibiotics kill most of your gut bacteria, allowing the somewhat better protected C. diff to proliferate, start producing toxins, and send you to the hospital with symptoms ranging from diarrhea to perforated colon and worse. That disease is a direct consequence of "Antibiotics kill some but not all bacteria in you".

microbiology - How to Diagnose this hepatitis A, B and C case?

The last sentence of the question doesn't make it clear what's being asked. But it seems to be asking: What version of Hepatitis did he get from the contaminated blood?

To that end...

Serum antigen of HB tells us about the levels of IgM and IgG. If vaccinated, then IgG should be positive, I think? What does HBsAg tell you?

HBsAg gives you the knowledge of whether or not there's an acute infection of Hep-B. Hep-B IgM antibodies indicate an acute infection, whilst IgG antibodies would show up due to his previous exposure/immunization. If the patient has Hep-B IgM, the icteric illness was probably a re-infection of Hep-B.

Why do we need to detect anti-HCV? If they are found, what does it mean? I think that then it means if found that he does not have hepatitis C then.

That would my assumption as well.

You run the HBsAg and can get two outcomes: IgM(+)/IgG(+) or IgM(-)/IgG(+). The former indicates the icteric illness was probably a reinfection of Hep-B.

You run the anti-HCV and get two outcomes: (+) or (-). The former indicates a present infection, the latter indicates no Hep-C.

What might throw you off is the wife's anti-HepC antibodies. If she was formerly infected and infected the patient (or vice versa) then you'd expect to find a (+) anti-HCV result.

I might come back to this after thinking on it a bit more, but that's the best I have for now.

zoology - Does sleep duration vary for animals based on time of the year?

I'm interested in the sleep patterns of wild animals, that still use sun for controlling their biological clock.

Animals entrain their biological clock to the day/night cycle using light as the entrainment signal. The biological clock follows the day/night cycle: dim light initiates melatonin secretion, while bright morning light stops melatonin production. Melatonin is involved in sleep regulation

Here, I have plotted the day duration over the course of the year for Northeast US, around Washington DC.

My question is given the day duration plot below, would the total sleep duration for wild animals vary over the course of the year?

In other words, would animals sleep longer in the winter time and shorter in the summer time?

If I graft two trees together while young, will they grow as one plant?

If two trees grow close enough together so that their trunks touch each other anywhere along the length of the tree, then they will eventually fuse. This generally only happens at the trunk because, unlike small branches, the trunk really can't be pushed out of the way as easily. It doesn't necessarily need to be two trees of the same species either.

There used to be a fused sycamore-maple on my school campus (it was damaged in Sandy and was cut down). They weren't completely fused together, but you could see a joint at the base and about 20 feet below the canopy where the trunks essentially became the same. There was no distinction between the two separate trunks.

But to finally answer your question; when the trees fuse they pretty much become conjoined twins. I'm not sure if they transfer genetics to each other, but they do share resources.

human biology - Lactose Intolerance

The lactose intolerance Wikipedia page explains the problem fairly well, so I'll refer you to that for a more detailed explanation.

Briefly, the most common cause of lactose intolerance is primary lactase deficiency, which affects the majority of the world's population. This only affects adults: the majority of people do not produce lactase as adults.

Congenital lactase deficiency, instead is a very rare, autosomal recessive genetic disorder that prevents lactase expression from birth.
[...]
Congenital lactase deficiency (CLD), where the production of lactase is inhibited from birth, can be dangerous in any society because of infants' nutritional reliance on human breast milk during their first months. Before the 20th century, babies born with CLD often did not survive, but death rates decreased with soybean-derived infant formulas and manufactured lactose-free dairy products. Beyond infancy, individuals affected by CLD usually have the same nutritional concerns as any lactose-intolerant adult.

A couple of good references:

Lactose intolerance in infants, children, and adolescents. - Heyman, Pediatrics 2006

Genetics of lactase persistence and lactose intolerance. - Swallow, Annu Rev Genet. 2003

neuroscience - Number of MHCs in neurons

Antigen presentation by MHC will induce a cytotoxic response by the immune system, which is usually a good thing in the body since most cells can just divide and replicate again. Neurons, however, are particularly ineffective at regenerating from such an attack, and are not easy to come by; they are also rather important! Better not to risk it, eh?

That being said, neuronal expression of MHC is actually a pretty complex case, and this open-access article is a good start down the rabbit hole (see also here, here, and here if you have access).

thermodynamics - How do warm-blooded animals keep their temperatures constant?

Since there seems to be several distinct sub-topics in your question, I will answer them one-by-one:

1). There are a variety of mechanisms that allow endothermic animals to maintain thermal homeostasis in a cold environment. The main ones are:

a). The shivering response: When the core body temperature of a endotherm drops below a critical value (36.8C in humans), it causes the posterior hypothalamus to stimulate certain skeletal muscle groups (especially around vital organs) to start to "shiver" rapidly, generating heat.

b). Compared to ectotherms, endotherms have more mitochondria per cell, thus allowing them to have a higher metabolism. Since metabolism always generates heat, an [general] increase in cellular metabolism will cause an increase in body heat.

c). Many endotherms have layers of insulating matter, such as fur, blubber, feathers…etc, allowing them to preserve body heat. In addition, endotherms can also route blood away from capillaries via vasoconstriction of arterioles, reducing the area in which heat can be lost.

d). As mentioned by Memming, brown adipose tissue also plays a role in temperature regulation. Thermoregulation-based metabolism in brown fat causes the P+ in the electron transport chain to go through thermogenin instead of ATP synthase. This process generates heat, but no ATP.

e). Some endotherms, such as penguins and arctic wolves have countercurrent exchange in their capillaries. This is when warm arterial blood "passes" some of its heat to cooler veinous blood. This feature allows some of the heat normally "wasted" into the air to be recycled back into the body.

Note: Though it is true that endotherms are able to keep their body temperature constant irrespective of their surroundings (ignoring extremes), they do this at a cost of requiring significant amounts sustenance. Most endotherms require much more sustenance than ectotherms.

2). Your second sub-question is very interesting. Though it is true that generating heat will require substantial amounts of carbohydrates/fats/...etc, it does not necessarily mean that the net consumption of sustenance in cold environments is greater than that in normal environments. In most cases, endotherms in cold environments will have exhibit significantly less activity than when in an optimal environment. The decrease in activity when in a cold environment will likely balance out the increase in thermo-regulation based metabolism. This likely explains why people tend to drink equal or slightly less amounts of water when in cold environments. One more thing: some reactions heat-generating reactions (like the alternate ETC pathway) do not require water. Glycolysis and Krebs actually generates water (not to say that there is a net gain in the body :))

3). In truth, nothing "prevents" ectotherms from generate heat. They simply do not have the cellular "machinery". Ectotherms metabolize in ways very similar to other organisms, using molecules like ATP, glucose, fat…etc. Unlike endotherms however, they spend very little of their energy on temperature regulation. As a consequence, their overall metabolic rates are dependent on the external temperature. The point is this: A substantial portion of endotherm sustenance is used to generate heat. Only a small (if any) portion of ectotherm sustenance is used to regulate heat. As a result, endotherms require much more nourishment than ectotherms.

4). I am not entirely certain what you mean by "evolutionary path", but I will just say this: In many ways, endotherms and ectotherms are organisms that have found different ways to the same problem; how to regulate body heat for maximal survival and reproduction. Basically,

ectotherm- more dependent on environmental temperature, requires less sustenance

endotherm- less dependent on environmental temperature, requires more sustenance

5). You are quite correct. The cellular and genetic components are very similar. Some morphological aspects seem to be shared as well.

Sources:

Cambell & Reece (2010) Biology (9th ed)

Swan, K. G.; R. E. Henshaw (March 1973), "Lumbar sympathectomy and
cold acclimatization by the arctic wolf", Analysis of Surgery 177 (3):
286–292,

Guyton & Hall (2006) Textbook of Medical Physiology. (11th ed)

Romanovsky AA. (2007). Thermoregulation: some concepts have changed.
Functional architecture of the thermoregulatory system. Am J Physiol
Regul Integr Comp Physiol. 292(1):R37-46.

chromosome - Coiling of chromatids during cell division

What is exactly coiling of chromosomes?
I just heard about the names i.e paranemic, plectonemic, orthostichious, anorthospiral.
I have ecaxtly no idea of what phenomenon is this.
Also what type of coiling occurs during meiosis and mytosis type of cell division.
Could it be explained in detail....?

cell biology - Experiments in vitro vs those with dead organisms and fixated tissue

Does the term in vitro necessarily imply that the organism/organs/cells of study are dead?

If not, is there an alternative latin term to refer to studies of dead biological matter ? (e.g. in Connectomics where the tissue is biologically dead, and has been fixated and sectioned with a microtome)

genetics - Non-monotonic knock-out effects in prokaryotes

Typically, when performing gene-knockout, the experimenters select one gene to remove/replace-with-junk and then see if the prokaryote can still undergo fission. If it continues to reproduce then the gene is labeled as non-essential; if the organism cannot reproduce then the gene is labeled as essential; and some-times (if the organism can reproduce but only for a certain number of generations) the gene is labeled as quasi-essential.

Typically, if gene X is essential, and you knock-out both gene X and some other gene Y then the organism still dies; this is an example of monotonic behavior. However, this doesn't always have to be the case, it could be that gene X is essential only in the presence of gene Y (for instance if the two proteins produced are in a delicate feedback loop). Is there examples when knocking out gene X makes the organism nonviable, but knocking out gene X and Y maintains viability? In the most extreme case, is there an example where both gene X and Y are essential, but if both are knocked-out then the organism is still viable? I am primarily interested in simple prokaryotes (an answer for Mycoplasma genitalium or Escherichia coli would be best) but more complicated organisms are preferred over no answer.

bioinformatics - Expanding the SETI initiative to seek intelligent data within DNA sequences?

Let's extend your idea a bit... Ok, there are conserved sequences that we may not know what their function is. Let's assume that they are indeed not functional and are some kind of message left by an ancient form of intelligence.

How would you go about detecting that? It is already given that they are highly non-random, but this is not surprising and many "non-message" sequences have this property. Also consider that these sequences are quite short, meaning that they will have low information content. This means that if you check enough conversion codes and use imagination, you would probably be able to find several "messages" which are "hidden" there (e.g. "bible codes" etc). In other words, as I am a scientist that deals with probability and pattern recognition frequently, you will have a very hard time trying to convince me that you found a real hidden message... Formally, you don't have a satisfying background model.

The main difference from SETI is that there they know that their background is essentially random noise, so it is much easier to detect "intelligent" messages.

microbiology - How do I measure bacterial growth in agar dishes (either by cell mass or by cell count)?

The most simple way is seeding the plates with a suspension of bacteria ensuring that you spread the solution properly. Then you can count the number of colonies, wich would be equal to the number of single cells.

If you want to mesure the growth speed, usually it's simpler to just measure the diameter of the colonies, always ensuring you inoculate the plates with the same amount of inoculum.

Lastly, it's even easier to estimate the growth if your culture is un liquid media and you measure the optic density with an spectophotometer.

genetics - How many nucleotide pairs code one gene?

You seem to have some confusion, so let's clear things up.

A gene is a stretch of DNA (or RNA) that codes for a polypeptide (protein), that is a series of aminoacids bound together.
Each gene consists of nucleotides bound together, which are interpreted by the cellular machinery in groups of three, called triplets.
DNA is first transcribed into messenger RNA (mRNA), which is then translated into proteins.
Each triplet codes for one aminoacid not one gene! In fact genes are not "coded" by anything, they are the code!

Now, what I just wrote is extremely simplified, there are other important details that I omitted, but hopefully it cleared your doubt.

To give you some further detail: not every single nucleotide in a gene will code for an aminoacid. There are regulatory elements such as the promoter of the gene, which allows the enzymes that transcribe the DNA to attach to the gene (essentialy it says: "hey, start transcription right here!"). Similarly, enhancers and silencers can tune up or down transcription of the gene.

In eukaryotes there are big stretches of DNA called introns that are not coding for anything but have big importance for regulating transcription. In fact a single mRNA can be used to code more than one protein, using a process called alternative splicing.

There are also regions of DNA that code for RNA sequences not translated into proteins at all, but which have all sorts of regulatory functions in the cell.

molecular biology - Should I design a primer to detect virus based on NCBI genebank?

Any other database better than NCBI ?

A lot of people overlook some sub-databases inside NCBI and search the main nucleotide database only.

If You never tried it, you can blast the HIV sequence which You have found, against other databases. On the ncbi blast webpage, just choose the options other than nucleotide collection (nr/nt). I tend to find new sequences in Expressed sequence tags (EST), Genomic survey sequences (GSS) or Whole genome shotgun contigs (WGS). Some of these databases cover unfinished sequencing project and should be a source of new data.

(I am a plant person, not virus person, so maybe you will find out, that different databases are worth searching for you. Or you will find it a waste of time.)

BTW, now some time had passed since your question. How did you solve Your HIV sequence problem ?

Recombinant protein fraction in E. coli

Miroux and Walker (1996) Over-production of Proteins in Escherichia coli: Mutant Hosts that Allow Synthesis of some Membrane Proteins and Globular Proteins at High Levels. J Mol Biol. 260: 289–298

The authors report on problems of over-expressing membrane proteins in E. coli using a T7 (pET) system. They isolate mutant strains which show improved levels of expression compared to the parent strain, BL21(DE3). In their Table 1 they document levels of expression of 17 proteins including, as a control, GFP. GFP was found as a combination of soluble and inclusion body protein at a level of 37 mg L^-1 in BL21(DE3) and 140 mg L^-1 in one of their mutant strains (C41(DE3)). The highest level of expression that they observed was 300 mg L^-1 for bovine OSCP.

Unfortunately the authors document neither the total protein content, nor the cell density of the cultures that they analysed.

Let's assume that the cultures were 10e9 cells mL^-1 = 10e12 cells L^-1.

According to this source (citing Neidhardt F.C. Escherichia coli and Salmonella: Cellular and Molecular Biology. Vol 1. pp. 14, ASM Press 1996), the dry weight of an E. coli cell is 2.8e-13 g

The generally accepted figure for protein as a fraction of dry weight in E. coli = 0.55

I calculate from these numbers a value of 1540 mg protein L^-1. For the three protein expression levels described above this means:

GFP in BL21(DE3) = 2.4%

GFP in C41(DE3) = 9.6%

bovine OSCP in C41(DE3) = 19.4%

I conclude (from these numbers, and from personal experience) that overexpression levels are highly variable, and are going to be strain and protein-dependent. Values in the range of 1-20% total cell protein may be anticipated.

evolution - Why don't all ants have wings?

When is it good to have wings?

When you need to move a great distance in as short a time as possible with minimal risk.

Clearly wings would have enormous benefit at a time when you need to get far away from the nest really quickly, perhaps at a time when you believe the weather would be particularly favourable. This benefit increases exponentially when procreation is involved.

When is it bad to have wings?

Almost any other time.

• When it is raining.

Rain and wings just do not go well together. If you get hit by a raindrop while wearing wings you are basically stuck where the drop lands until it evaporates completely.

• When it is windy.

I rest my case.

• When you are under attack.

Agility, while wearing wings, just cannot be considered one of your evolutionary advantages.

• When you are trying to gather/carry food back to the nest.

Surely an ant trying to carry a piece of a leaf, however small, would consider wings a severe burden.

• When times are hard foodwise

The protein investment in wings would surely be better spent on survival when food is scarce.

• Encounters with birds suck

Wings make you incredibly easy to grab hold of in mid-air, unless of course you can shed your wings when stressed, and many ants can (while obviously butterflies and moths cannot).

Surely my arguments suggest that having no wings would be a serious advantage in almost any situation except on the rare occasion when you need to move a long way really fast. Clearly the ant has an amazing skill to only have wings when they are needed and not at any other time.

Added after a number of comments

You have to remember that much of an ant's work is maintaining the colony as a collective. Preserving its cohesion, feeding the young, caring for eggs. The whole point of having a colony is to have far fewer individuals spread out, in danger, gathering food. This is to reduce the risk of complete colony death, which is essentially the death of the queen and therefore the gene pool of the colony.

You have to look at each ant colony as a single individual when you look at them on an evolutionary scale. In this way the life or death of one, or even 1,000 ants is not important, it is the survival of the colony. From this perspective, wings are dangerous for all my reasons above. The only time they are of value is during diaspora and that is the only time ants have them, which I think is incredibly clever.

Evolving a detachable appendage to an ant is like humans evolving detachable breasts at menopause. An astonishing achievement even humans have failed to achieve.

human biology - Do hormone drugs affect whether a person feels sexual attraction to males or females?

I know that ingesting testosterone and other hormonal drugs may stimulate libido and increase sexual desire.

But I wonder, if a man ingests female hormones such as estrogen, will he experience sexual desire towards other men or not?

Similarly, the other way around, whether a female ingesting male sexual hormones will experience desire towards other women?

The question is motivated by the interest to know whether transgender people, particularly, the MtF transsexuals engaged in prostitution experience genuine attraction to males.

digestive system - Long term liquid food diet by blending/grinding all quality foods one would normaly eat, not any weight loss or prepared drinks

I want to know what are the effects of not using your teeth to grind foods but preparing it before eating with blending and grinding them into a liquid.

Here I am not talking about any weight loss or fitness industry prepared drinks. I mean the ordinary raw and cooked foods like meat, vegetables, cereals, and fruits that one would normally eat in classic meals.

Would this decrease of work done by teeth and digestion system have positive or negative health effects?

human biology - Where does all the food go?

Whatever the diet, the food intake contains macronutrients: carbohydrate, fat and protein. When they are metabolised all of these molecules will end up, for the most part, as carbon dioxide, water, and ammonia, unless they are incorporated into components of the body.

These waste products are, of course, lost via breathing, and via the urine. That's where the "missing mass" goes.

A related question is here.

microbiology - How was the diversity between ethanol fermentation and lactic acid fermentation evolved?

First, it is not clear from the physiology or biochemical information alone to determine what evolved from what. The intermediate pyruvate is always there, so lactose dehydrogenase (LDH) and pyruvate decarboxylase (PDC) could have each evolved anytime, and there are good reasons for both:

1. LDH: the reaction pyruvate + NADH/H+ = lactate + NAD+ + 25 kJ/mol is highly exergonic, i.e. produces heat


2. PDC: the reaction pyruvate = acetaldehyde + CO2 (and with ALD present) acetaldehyde + NADH/H+ = ethanol + NAD+ where ethanol is poisonous to other species

Add to it that there are organisms like Sch. pombe that have both enzymes, so can do both reactions, your questions should be rather:

How has the enzyme LDH evolved?

The enzyme is similar to malate dehydrogenase, both form a family. They belong to a group of enzymes that all have a NAD(P) binding domain, so it's not too far-fetched to state that LDH and MDH evolved from another enzyme with NAD(P) binding domain.

http://www.ebi.ac.uk/interpro/IEntry?ac=IPR016040

How has the enzyme PDC evolved?

Protein sequences of pyruvate decarboxylase (PDC) derived from cloned
yeast (Saccharomyces cerevisiae) and bacterial (Zymomonas mobilis)
genes were compared with each other and with sequence databases.
Extensive sequence similarities were found between them and with two
others: cytochrome-linked pyruvate oxidase from Escherichia coli and
acetolactate synthase (ilvI in E. coli; ILV2 gene in S. cerevisiae).
All catalyse decarboxylation of pyruvate using thiamine pyrophosphate
(TPP) as cofactor. General overall similarity suggests common ancestry
for these enzymes.

cited from abstract of

Green, Jeremy. "Pyruvate decarboxylase is like acetolactate synthase (< i> ILV2) and not like the pyruvate dehydrogenase E1 subunit." FEBS letters 246.1 (1989): 1-5. http://www.ncbi.nlm.nih.gov/pubmed/2651151?dopt=Abstract

How essential is vitamin B3 to the diet?

According to one study:

It was calculated that if the excretory percentage of niacin metabolites in the urine were 60%, of the tryptophan ingested, the conversion factor would be a value of 67, meaning that is 67 mg of tryptophan is equal to 1 mg of niacin.

However, the study has a pretty low power with only 10 participants and an indirect measure of niacin.

Is it possible that a person could get all of their niacin from tryptophan? Probably - you just need to eat enough tryptophan, which is also an Essential Amino Acid. The body may preferentially keep Tryptophan (which it does not store) until Niacin runs out (which also cannot be stored).

organic chemistry - What is the effect of flash pasteurisation on Maillard reactions or production of AGEs in milk?

This is only an partial answer, as I do not have the time now to look for other references.

In the chapter about milk, Harold McGee's beautiful book "On Food & Cooking" says (pg. 21 of the 2004 edition, bold is mine):

Flavors from cooking
Low-temperature pasteurization slightly modifies milk flavor by driving off some of the more delicate aromas, but stabilizes it by inactivating enzymes and bacteria, and adds slightly sulfury and green-leaf notes (dimethyl sulfide, hexanal). High-temperature pasteurization or brief cooking - heating milk above 170°F/76°C - generates traces of many flavorful substances, including those characteristic of vanilla, almonds and cultured butter, as well as hydrogen sulfide. Prolonged boiling encourages browning or Maillard reactions between lactose and milk proteins, and generates molecules that combine to give the flavor of butterscotch.

He continues by speaking about the different types of pasteurization, and says (pg.22-23)

The third method of pasteurizing milk is the ultra-high temperature (UHT) method which involves heating milk at 265-300°F/130-150°C either instantaneously or for 1 to 3 seconds, and produces milk that, if packaged under strictly sterile conditions can be stored for months without refrigeration. The longer UHT treatment imparts a cooked flavor and slightly brown color to milk; cream contains less lactose and protein, so its color and flavor are less affected.
Sterilized milk has been heated at 230-250°F/110-121°C for 8 to 30 minutes; it is even darker and stronger in flavor, and keeps indefinitely at room temperature.

So, it appears as if indeed there may be some Maillard reaction going on in UHT, although it is probably minor (otherwise the milk would be much darker in color, as it is the case for sterilized milk).

The book also speaks about homogenization, but it does not mention anything specific about Maillard reaction there (homogenization is not carried on at high temperatures, so it does makes sense not to have it).

To answer your question:

Does this effect the nutritional value of the milk?

Well, according to this presentation (but, be warned, it does not cite any reference!) it seems that it does, although I don't think the Maillard reaction is specially involved.

http://www.slideshare.net/Aslal_saja/effect-of-uht-treatment

Specifically it says that the irreversible changes that occur are:

• Whey protein denaturation (35 to 100% of denaturation of $\beta$-lactoglobulin)


• Slight increase in the size of casein micelles


• Whey protein-casein micelle interaction


• Maillard reactions


• Fat globule composition changes (although no changes in nutritional value of milk fat)


• Vitamin content changes (20-30% loss in vitamin B1 and B12. Markedly reduced content in vitamin C and folic acid if high level of oxygen were present during the treatment, no changes in vitamins A, D, E and beta-carotene).

It also says that:

Biological value and net protein utilization of UHT milk were lower for stored milk than directly used milk. Lysine loss during UHT is high but not significant to affect milk nutritional values.

---

I don't know whether the fact that you have problems when drinking UHT milk has anything to do with Maillard reaction or any of the other modifications brought by UHT treatment, and I will not venture in there, as I am not an MD and prefer not to give any sort of medical advice.

cardiology - How quickly can the human heart rate rise and fall?

How quickly can the human heart rate rise and lower?

For example lets say a human heart rate is rested and is at 60BPM and that person is suddenly scared to trigger their fight or flight reaction. Lets say their heart rate rises to double (120BPM).

From the above example their rate has gone from 1000ms between beats to 500ms between beats. Can the human heart instantly in one heart beat go from the 1000ms to 500ms between beats or does it need to ramp up? If yes how quickly can the heart rate ramp up?

I understand that each human heart is different, and that the speed increase and decrease will be different from person to person. What I'm looking for is a value that I can safely say the human heart won't exceed.

Similarly the same question goes to your heart going lower.

genetics - Knockdown of long noncoding RNA (lncRNA) - how is it done?

Knockdown of lncRNA in mammals is not done via RNAi. Instead, one transfers antisense DNA oligos which bind to the RNA. This triggers the action of the RNase H enzyme, which degrades RNA-DNA duplexes. It degrades the lncRNA.

UPDATE: For reference, I learned about this from a seminar, and it is not very well documented, but after some literature search I found this paper to quote:

Although we (Fig. 3A) and others (42, 49) have used siRNA to knock down NEAT1 lncRNA and although the knockdown of strictly nuclear RNAs has been well described (53, 54), we remained concerned that because NEAT1 is mostly a nuclear RNA (55), it may not be very efficiently targeted by the RNAi machinery. Nuclear RNAs, however, are proficiently targeted using complementary antisense (AS) oligodeoxynucleotides that recruit nuclear RNase H activity to degrade the RNA (56). Hence, we also employed complementary AS oligodeoxynucleotides to knock down NEAT1 lncRNA in HIV-1 NL4-3-infected Jurkat cells (Fig. 4C, left). The AS approach reduced NEAT1 (Fig. 4C, left) and increased HIV-1 p24 production (Fig. 4C, right), providing results consistent with those from siRNA-mediated knockdown of NEAT1 (Fig. 4A and B).

neuroscience - What happens during a Raynauds episode?

Raynaud's phenomenon can be a serious health issue, as the blood flow to the extremities, mainly the fingers is compromised, causing fingers to blanche, and then turn blue. Severe Raynaud's can cause gangrene in illnesses like progressive/ diffuse scleroderma.

I am not asking about connective tissue disease per se, but what occurs during an actual Raynaud event (for a better way of putting it), not what precipitates the condition to occur within a particular person and not another.

what are the underlying biological processes that cause the blood flow to be compromised like this?

zoology - Is there such thing as "meters per calorie" for living organisms?

Halsey & White (2012) Comparative energetics of mammalian locomotion: Humans are not different. Journal of Human Evolution 63:718–722

This paper presents a comparison of the metabolic cost of walking and running in humans, Australopithecus and other mammals. They use a parameter NCOT (net cost of transport), whose units are ml O₂ consumed m^-1. The inverse of this parameter would be related to your metres per calorie.

The authors quote an NCOT of 12.77 ml O₂ m^-1 for a walking human. Using a value of 4 kcal g^-1 for glucose, I calculate that this NCOT is equivalent to 14.6 m kcal^-1.

Here I found an energy consumption value of 5.8 kcal min^-1 (for a 73 kg man) walking at 6.4 km h^-1, which translates to 18.5 m kcal^-1.

Incidentally, according to the authors of the paper:

The predicted net cost of transport (NCOT, ml O₂ m⁻¹) of mammals is related to mass (M, kg) according to 0.54M^0.70.

human biology - Does the brain and the body use the same energy source (glucose/ATP)?

While in general the answer is "yes", the brain does use the same type of resources as other parts of the body, you cannot from that alone derive conclusions about the brain competing with other organs. Also, I think that cognitive performance is not a function of availability of resources. In fact, the moment that the brain lacks crucial resources like oxygen, it simply shuts down. But you don't faint when you start running (if you do, go see a doctor). "Power-saving mode" for the brain is not "reduce IQ by 20 points", but "just make sure the body is breathing and shut down everything else".

Also, I do not think that digesting food requires any comparable amount of energy that it would require the brain to give up on some of the oxygen it needs.

evolution - Why is duck fat less saturated than cow fat?

Because ducks need to float and cows don't. If there was a densely fat duck it wouldn't float or fly very well and it wouldn't survive to reproduce.

To answer your question, the composition of fat varies because of the different conditions in which the organism needs to thrive. Fur is different as well. Bear in mind nature is a cruel place and any tiny edge you can get is vital for your survival.

My answer is a bit general but I hope it addresses the question.

By what mechanism does elevated homocysteine level accelerate thrombin formation?

According to a heavily-cited paper (below), homocysteine reduces the expression of thrombomodulin on the surface of endothelial cells.

Thrombomodulin binds to thrombin, and the resulting complex does not promote coagulation, but instead activates protein C. Protein C has an anticoagulant effect. Thus reduced levels of thrombomodulin will result in increased levels of free thrombin (promoting coagulation) and in reduced levels of protein C (also promoting coagulation).

I haven't found any evidence that homocysteine has an effect upon thrombin formation directly.

Lentz,SR and Sadler, JE (1991)Inhibition of thrombomodulin surface expression and protein-c activation by the thrombogenic agent homocysteine. J. Clin. Invest. 88:1906-1914

Abstract Elevated levels of plasma homocysteine are associated with both venous and arterial thrombosis. Homocysteine inhibits the function of thrombomodulin, an anticoagulant glycoprotein on the endothelial surface that serves as a cofactor for the activation of protein C by thrombin. The effects of homocysteine on thrombomodulin expression and protein C activation were investigated in cultured human umbilical vein endothelial cells and CV-1(18A) cells that express recombinant human thrombomodulin. Addition of 5 mM homocysteine to endothelial cells produced slight increases in thrombomodulin mRNA and thrombomodulin synthesis without affecting cell viability. In both cell types, thrombomodulin synthesized in the presence of homocysteine remained sensitive to digestion with endoglycosidase H and failed to appear on the cell surface, suggesting impaired transit along the secretory pathway. In a cell-free protein C activation assay, homocysteine irreversibly inactivated both thrombomodulin and protein C in a process that required free thiol groups and was inhibited by the oxidizing agents diamide or N-ethylmaleimide. By inhibiting both thrombomodulin surface expression and protein C activation, homocysteine may contribute to the development of thrombosis in patients with cystathionine beta-synthase deficiency.

biochemistry - Does animal fat and meat contributes differently to our body?

Have you read the Wikipedia article on Fat? It has literally all of the answers you are seeking. However...

1: Every single thing is bad for you if you get too much of it. Animal fat, sugar, water, you can over-do it on anything. Fat can be bad for you but it is definitely required. In particular, "Vitamins A, D, E, and K are fat-soluble, meaning they can only be digested, absorbed, and transported in conjunction with fats. Fats are also sources of essential fatty acids, an important dietary requirement." Fat does a host of other things, as mentioned in the article.

2: Fat is indeed a concentrated store of energy, but there's more to life than just energy. Protein, like other nutrients, are required for life. Protein happens to be particularly important, providing the structure for all our cells, is required for muscle growth, and provides amino acids, which are needed to make other proteins in your body. Proteins are used as hormones, cellular messengers, immune receptors, so on and so forth. You couldn't live without protein. Energy, while concentrated in fat, could come from elsewhere.

3: It worked just the same for them as for us. I will add, however, that our ancestors did not necessarily use every part from every animal, and these days, we actually use every part of many animals, just not always for food.

4: Sure? Energy is good, but protein is probably better. "Athlete" is a vague term, as strength-training and endurance activities are very different from each other. Protein is probably better for strength, carbohydrates are probably better for endurance. But you can ask over at http://fitness.stackexchange.com/.

ornithology - Identify this waterfowl species?

I've been unable to find anything on the Google resembling this bird. I took the photo in Virginia Beach, VA around 2010, October, I think...
It appears to be between winter and summer plumage but I'm not sure. I tried looking on whatbird.com but couldn't find anything that really seemed to match up well.

Edit

I've added some more photos since people seem to question whether or not the white is snow, for some reason. Also note that most seem to have a red bill with a black tip, while the one with more white on its breast has a largely black bill with just a red band. Do bills change colors when plumage does, is that a thing, or perhaps it's just an anomaly or a gender trait?

Why does contracting the iris allow less intense light to go in?

Imagine the iris like a shutter in front of a focussing lens (which, in fact, it is; see the diagram).

This means that any light going through the iris will be focussed on a very small point on the retina, and your eye is wonderfully developed in a way that this exact spot is the fovea, the only spot in the retina that allows you to see colour and high-resolution.

The iris does not modify the focussing function, it merely changes the amount of light going through into the lens to then be focussed onto the fovea. Imagine that every single object in your field of view reflects/radiates light in every possible direction - narrowing the shutter won't exclude parts of the field of vision, it will only exclude some of the rays coming in at very flat angles and thereby reduce intensity.

Only if your lens is deformed, focussing (adaptation) will malfunction (directing the gathered light to the wrong spot; or focussing the incoming light in front of or behind the retina) and blur your vision.

human biology - Why does air from the nasal cavity not go into the oesophagus?

Swallowing food requires muscle strength to force the food down the oesophagus, which is a soft tube that collapses when empty, simply because the body is very crowded (space-efficient) and empty spaces collapse unless forced open. Only when you swallow, the oesophageal muscles force space to be made for food coming through.

In contrast, the trachea and bronchi are covered in almost-circular or C-shaped cartilage which holds them open and stable for air to flow through. You can see it here: http://en.wikipedia.org/wiki/Bronchi.

Concluding, air does not enter the oesophagus because it is always closed. Additionally, when the chest expands for breathing, the lungs expand and create suction down the trachea and not into the stomach (simply because this is where they connect).

The exception of course is if air is trapped in the swallowing motion with (or without) food. In this case it will enter the oesophagus and cause you to burp.

cellular respiration - Why do red blood cells contain haemoglobin and not myoglobin?

Just to expand slightly on the answer by Jack Aidley:

Have a look at this section from Stryer's Biochemistry text book, particularly Fig 10.17, where you can see that haemoglobin has evolved to have a high affinity for oxygen at the O₂ concentrations present in the lungs, but a low affinity at the O₂ concentrations present in the peripheral tissues. This is achieved by binding oxygen co-operatively. This means that haemoglobin can release 60-70% of its bound oxygen. Under the same conditions myoglobin, were it be used in red blood cells as an oxygen carrier, would release much less.

Incidentally the Figure linked to shows a comparison between haemoglobin and a hypothetical protein which shows 50% saturation at the same concentration of oxygen but which binds oxygen non-cooperatively (like myoglobin).

A more direct comparison of haemoglobin and myoglobin - found here - is shown below:

edit added to respond to shigeta's response

I don't understand some of the statements from shigeta so here are my views - if I am wrong, I would (genuinely) like to be corrected, since I have to teach this stuff.

..."what is particularly useful about Hb's cooperativity is that the last oxygen is harder to pull off the Hb tetramer than the first."

This statement contradicts my understanding of the oxygen-binding behaviour of haemoglobin. In the deoxygenated state the protein is in the conformation known as the T (for tense) state, and this is a low affinity state. The binding of an oxygen molecule to one of the haem groups in one of the globin subunits of the tetramer increases the affinity, so that subsequent binding of oxygen becomes easier. The details of how this happens are still debated, but I think what I have said so far is accepted by everyone.

Here is an equation to represent the binding of the first oxygen molecule to the haemoglobin tetramer:

O₂ + [Hb]₄ <--> [Hb₄]O₂

If deoxygenated Hb has a low affinity for oxygen then that equilibrium must lie to the left hand side - in other words the right to left reaction (release) is faster than the right to left reaction (binding). This is not consistent with the idea that haemoglobin hangs on to its last oxygen.

"The heart, which is the first organ in the blood cycle after the lungs uses a lot of oxygen - if hemoglobin were not cooperative, it might take all the oxygen from hemoglobin just after the beat when it uses oxygen when in distress, creating a block of hemoglobin which is completely without bound oxygen."

This is based on an erroneous view of the circulation - it implies that all of the blood passes through the coronary artery before getting to the rest of the body. Oxygenated blood leaves the heart via the aorta. Although it is true that the first branch off the aorta is the coronary artery, most of the blood doesn't enter this branch, but proceeds into the remainder of the circulation. In this sense the coronary circulation (by which I mean coronary artery>coronary veins - the heart's own blood supply) is in parallel with the rest of the circulatory system, not in series with it. At rest, just 5% of the heart's output goes into the coronary circulation.

According to this review, Regulation of Coronary Blood Flow During Exercise, (I am simplifying a lot here, but this statement does appear in the review and is not taken out of context): "Increased myocardial oxygen demands during exercise are met principally by augmenting coronary blood flow." At rest the heart is already extracting most of the oxygen from its blood supply (see here for some interesting data) so again there is no question of the heart extracting much more - it simply needs more blood, and of course the increased heart rate will contribute to this. There is also scope for directing a greater proportion of heart output through the coronary circulation, but I have been unable to find any quantitative statements about that. Interestingly, if you take a look at the data in the 1st table of the data here you will see that, at rest, 22% of the heart's output goes into the renal circulation, but that much less oxygen is extracted from that blood (about one ninth of how much is extracted from the blood going through the cardiac circulation). This represents a source of potential increased blood to be diverted to the heart at the expense of a reduction in renal filtration.

"Also - Hemoglobin is pretty clearly an evolutionary adaptation where four myoglobins came together to form a cooperative oxygen binder, so at one time probably myoglobin was the oxygen carrier. There are some primitive animals which have no distinct hemoglobin, just myoglobin like carriers."

I agree it is clear that haemoglobin and myoglobin evolved from a monomeric myoglobin-like ancestor, and that the appearance of a tetrameric molecule created the potential for co-operative oxygen binding. I am not as convinced by the rest of the sentence. I think we have to agree first on what we mean by an oxygen carrier. What I mean is a protein that is a component of a circulatory system. I know of no evidence that a myoglobin like molecule could perform this function. This arises directly from the shape of a simple binding curve (a rectangular hyperbola). For the protein to be saturable at atmospheric oxygen concentrations it has to have a certain K_d, and this precludes significant release of oxygen at physiologically useful concentrations. You either have a protein which can unload effectively but will not ever become saturated with oxygen, or you have a molecule that is able to become saturated but cannot ever unload except at every low oxygen concentrations. That is the remarkable thing about haemoglobin - the appearance of cooperative binding allowed for a more switch-like interconversion between a high affinity state, for loading up, and a low-affinity state, for unloading.

Now, if you wish to include intracellular oxygen transport in your definition of "carrier" then we enter a whole other debate about the role of myoglobin, but I have gone on for far too long already, so I'll stop there.

entomology - Are there any solitary species of ant or termite?

The social insects consist of the ants, the bees, and the termites, which live in colonies rather than living solitary.

But I've heard that there are some species of bee which are solitary and don't live in colonies.

Are there also any species anywhere of either ants or termites which are solitary?

genomes - issues with MultiPipMaker

I would like to use MultiPipMaker for testing a genome alignment between two sequences, each sequence is in .fasta format, but the problem is that when I submit the couples of file that I need, the web browser sends an email that the blastz has timed out. Does anybody know why is the that?

The address of the program is:

http://pipmaker.bx.psu.edu/cgi-bin/multipipmaker

thanks

lab techniques - How can I resuspend a cell pellet without harming the bacteria?

When using a preculture with Ampicillin in my protein expression, I have to get rid of the preculture medium to avoid carrying over too much beta-lactamases that will destroy the ampicillin in the main culture. To do this I pellet the cells and resuspend.

Which methods of resuspension are best suited if you need the bacteria alive afterwards? I'm not sure how much force I can apply without harming the bacteria, and resuspending very gently takes a very, very long time.

Which methods can be used to resuspend bacteria alive, and which ones are the fastest?

human biology - fibroblast cells and fibers

Regarding dimensions:

As per this image the length and breadth seems to be ~30-50 μm (area should be roughly around 900 μm²). The third dimension (thickness) as per this article can be assumed to be around 3-7 μm.

Regarding cell attachment:

Cells attach to extracellular matrix via integrins, which attach to ECM proteins like collagen and fibronectin. The matrix is a net of fibres and the cell is not specifically attached to a single fibre but rather "sits"(as you said) on the matrix [see the below image]. A single cell also simultaneously interacts with two different types of ECM proteins such as fibronectin and collagen.

During migration they move along the matrix using lammelipodia (actin filament polymerization in the direction of motion).

Fibroblast express ICAM1/VCAM1 (Inter/Vascular Cell Adhesion Molecules) under certain conditions such as inflammation and bind to T-cells and endothelial cells.

entomology - Identification of an Insect (Hemiptera)

I found a a few of these guys on my composter, so they could have easily been eating bugs or decaying organics (or both):

To me it looks like a stink bug with oversized legs, not like the ones I'm used to seeing. His body measures just under 3cm, and I haven't pulled on his legs to get a measurement (I haven't pulled on it at all). The legs seem to be at least 1.5 times the body length as do the antenna. The body is grayish brown and the antenna and parts of the leg seem reddish brown.

I'm a microbiologist, so things big enough to see in a jar are not really my specialty. That said, here's info that I've been trying to use ID it:

Wingless Normal compound forelimbs (don't seem to have any kind of prey modification)

Segments filiform antenna (I think)

2 Tarsomeres (I think)

In the middle of South East US

Have had (unusually) heavy rains

Underside of the limbs and antenna seem red, but to seems gray

I've never seen it before! (and I usually notice such things).

Update: Despite my 4 year old putting other bugs and some leaves in with it, the bug died. I took the opportunity to get some much better photos, and low and behold when I started manipulating it I was able to pull out a substantial rostrum that I missed! These guys are good at hiding those. So going back to assassin bugs, can anyone id which assassin bug it is?

More photos: [I would add more but I think this should be plenty]

I at least think it's quite a pretty specimen (to betray my mammalian aversion to bugs).

physiology - What causes the characteristic 'gleam' in the eye of a living being?

Not being an opthalmologist, if one happens along and gives a better/correct answer, listen to them.

Otherwise, let's take a moment to look at the eye:

What is not pictured here is the saline-like solution that keeps the conjuctiva moist. If we include the lubrication in all of the surfaces which interact with light, our list would look like this:

• Lubrication


• Conjuctiva


• Cornea


• Anterior aqueous humour


• Iris


• Posterior aqueous humour


• Lens


• Vitreous humour


• Retina


• Fovea

Out of that list, the Iris, Retina, and Fovea are designed to absorb light; not reflect it. The Vitreous humour merely serves as a medium for light to pass through and probably would not reflect light on its own. The same is true of both aqueous humours - they do not modify the light so much as serve the eye structurally.

That leaves us with the Lubrication, Conjuctiva, Cornea, and Lens - surfaces which also interact with light, but act to some extent to reflect or modify it as well. The Cornea is what's actually operated on when a person undergoes corrective surgery; a pattern is etched into the Cornea which redirects light similar to the person's previous prescription and giving them better vision.

Now, because you mention the difference between an excited person and presumably someone at their normal state, it's worth to note (when dealing specifically with the eye) a very common side-effect of psycho-active drugs and emotional states (particularly fear and interest/curiosity) is the change in pupil size when lighting conditions don't change:

The reflection is different depending on the size of the pupil, and I would venture to guess the pupil size difference between someone who's excited or manic (whose system is flooded with endorphins) and the person at normality is part of what you define as 'gleam.'

The other situation you draw a difference between is a dead person vs. a living person. Before rigor mortis sets in, the relaxed state of the ciliary body is to stress the suspensory ligaments - resulting in pupil dilation. In addition, and I think this is the most important distinction: dead people don't blink. The act of blinking spreads the lubrication on the surface of the conjuctiva, and can be mimicked with tear-drops for people with dry eyes. Because the lubrication acts as another surface to reflect light (similar to having a thin layer of water on a surface), the dead person's eyes will have less of a "gleam" than a living person's.

So, to sum up: The "gleam" in a person's eye is probably due to hydration and/or pupil dilation. Pupils will dilate at lower light levels, under the influence of certain drugs, or when showing interest. Hydration is constant, except when the lubrication is not produced in the quantities necessary or when the person is unable to blink ('dead' in your example).

evolution - When has an organism evolved enough to be called a new species?

I think LuketheDuke's answer is an oversimplification of the biological species concept (possibly resulting from the dictionary having a poor definition). The definition he gives is one of many which are in current use, and is made redundant by many types of organism.

It is important to recognise that because reproduction is not the same process in all organisms, genetic differentiation between individuals occurs in different ways for different groups.

Let's take the definition given in LuketheDuke's answer...

The major subdivision of a genus or subgenus, regarded as the basic category of biological classification, composed of related individuals that resemble one another, are able to breed among themselves, but are not able to breed with members of another species.

Under this definition, lions and tigers (see ligers and tiglons, which are sterile hybrids between the two) would be considered one species, as would donkeys and horses (see mules and hinnys, again sterile hybrids). There are hundreds of other examples of pairs of animal species which can hybridise to produce sterile offspring.

However, these animal hybrids usually only take place with human intervention, by delibrate breeding efforts. Thus we could extend the previous definition to include them...

The major subdivision of a genus or subgenus, regarded as the basic category of biological classification, composed of related individuals that resemble one another, are able to breed among themselves, but do not breed freely with members of another species in the wild.

That last part takes care of the ligers and tiglons. But what if we consider plants? Under the definition I just gave, most grasses (around 11,000 species) would have to be considered as one species. In the wild, most grasses will freely pollinate related species and produce hybrid seed, which germinates. You might then think we could just modify the definition to specify that the offspring must be fertile (i.e. able to reproduce with one another)...

The major subdivision of a genus or subgenus, regarded as the basic category of biological classification, composed of related individuals that resemble one another, are able to breed among themselves, but do not breed freely with members of another species in the wild to produce fertile progeny.

Unfortunately, the situation is still more complicated (we've barely started!). Often wild hybridisation events between plants lead to healthy, fertile offspring. In fact common wheat (Triticum aestivum) is a natural hybrid between three related species of grass. The offspring are able to breed freely with one another.

Perhaps we could account for this by taking into account whether the populations usually interbreed, and whether they form distinct populations...

The major subdivision of a genus or subgenus, regarded as the basic category of biological classification, composed of populations or meta-populations of related individuals that resemble one another, are able to breed among themselves, but do tend not to breed freely with members of another species in the wild to produce fertile progeny.

This accounts for the grasses, but it still leaves a messy area when you have a hybridisation which establishes - until the hybrid population is segregated away from the parent populations it is unclear whether they still count as the same species.

We could probably live with this situation, except for the fact that bacteria refuse to conform to it at all. Bacteria of the same species, or even very different species, can freely transfer genes from one to the other in conjugation, which combined with fission can result in perfectly replicable hybrids. This is such a common occurence that it breaks even the 'tend to' part of the previous definition, and members of a population can be doing this almost constantly, which negates the segregation requirement.

Richard Dawkins had a go at defining around this, by stating that...

two organisms are conspecific if and only if they have the same number of chromosomes and, for each chromosome, both organisms have the same number of nucleotides

This partly gets around the bacterial problem and means that bacteria which result from conjugation are a new species. Unfortunately under this definition we might as well not ever bother trying to classify bacteria as billions of new species would be created every day - something which the medical profession might have something to say about. This definition would also mean that those with genetic diseases like trisomy 21 are not human. The final nail in the coffin of this attempt is that there are many species, including frogs and plants, which are very certainly considered a single species by taxonomists but which have some variety in the presence of small accessory chromosomes, which occur in different combinations between individuals.

Let's consider one last option. We now live in the era of genomics where data about genomes of thousands of organisms is accumulating rapidly. We could try to use that data to build a species definition based upon similarity at the nucleotide level. This is often used for bacteria, by considering organisms with less than 97% nucleotide similarity to be different species.

The major point I've been trying to make, though, is that species is not a natural concept. Humans need to be able to classify organisms in order to be able to structure our knowledge about them and make it accessible to people trying to link ideas together. But the natural world doesn't care about our definitions. Ultimately the species concept is different for different groups of organisms and will continue to change over time as our analytical methods and the requirements of our knowledge change. Note that I've deliberately skipped over many historical species concept ideas.

The direct answer to your horse question is "it depends how you want to define a horse".

death - molecular indicators of apoptosis: clarification needed

Although both involve DNA fragmentation, the pattern produced is very different. During apoptosis, DNA fragmentation is done in a regular, controlled pattern, which if run on a gel produces a characteristic "ladder" pattern. Necrosis, on the other hand, is a more stochastic process, and will produce a smear. This details the difference rather nicely, including different ways to assay for either one in table 18.3.1 such as morphological staining or flow cytometry.

Here's a nifty image from the link. Figure 18.3.2. M is the marker, and in panel A, a conventional gel, lane 1 is apoptotic DNA, lane 2 is unprocessed DNA, and lane 3 is necrotic DNA. In panel B, a pulsed-field gel, lanes 1 2 and 3 are untreated, apoptotic, and necrotic, respectively.

endocrinology - Prostaglandin F2-alpha production in men

As I know:

One of the most important chemical mediators are prostaglandins that in vivo act on different cell receptors and have different effects on the body. Prostaglandins are twenty-carbon lipid molecules and structurally similar to cholesterol. Prostaglandins have different types, such as F2, E2 alpha, PGI2, and so on.

A phospholipase enzyme converts phospholipids of cell membranes into arachidonic acid. The arachidonic acid within the cyclooxygenase enzyme or Cox (both type 1 and 2) can be converted to prostaglandins.

PGF2alpha has functions in uterus contraction and bronchoconstriction, so I think both uterus and lung cells produce it.

I have no special information about production of PGF2alpha in men.

entomology - Is it true that there is a spider that eats parasites from caterpillars

Oddly enough it is a bit difficult to find good field studies where the diet of spiders was studied. I have a feeling it's a hard thing to get funding for. Luckily some do exist.

Peucetia viridans has been shown to eat from the Chrysididae family and Lepidoptera order, but I didn't find an explicit statement that it ate the larvae out of the caterpillar. Likewise Oxyopes globifer was found to have eaten from the Braconidae family and Lepidotera.

At this point you might be wondering why I'm looking for spiders that have been shown to eat both parasitoids (Chrysididae and Braconidae) and caterpillars (Lepidotera). It my assumption that in the scenario you describe a spider that would normal eat ether the caterpillar or the larvae would be just as happy to eat them both if it was lucky enough to find them.

I could find one example where it seems wolf spiders under the right conditions might seek out larvae, and I found a fun photo of a wolf spider eating larvae (though not the kind in the study).

I never saw the video you were talking about, and I too could not find it. It is not unreasonable to assume that an opportunistic spider wouldn't just take the opportunity to feed on both, or that it might find the larvae more tasty and just eat them. I've not found a spider seeking caterpillar as of yet.

bioinformatics - What is the potential function of ultra-conserved elements in the genome?

Probably development, in particular transcriptional regulation. To quote each link in turn,

They are found in clusters across the human genome, principally around genes that are implicated in the regulation of development, including many transcription factors. These highly conserved non-coding sequences are likely to form part of the genomic circuitry that uniquely defines vertebrate development.

and

[Highly conserved non-coding sequences] are significantly associated with transcription factors showing specific functions fundamental to animal development, such as multicellular organism development and sequence-specific DNA binding. The majority of these regions map onto ultraconserved elements and we demonstrate that they can act as functional enhancers within the organism of origin, as well as in cross-transgenesis experiments

Additionally,

Here we report that 45% of these sequences functioned reproducibly as tissue-specific enhancers of gene expression at embryonic day 11.5. While directing expression in a broad range of anatomical structures in the embryo, the majority of the 75 enhancers directed expression to various regions of the developing nervous system.

These regions tend to be highly clustered in around 200 areas, and most of them are non-coding. ncRNA is often regulatory, and those UCE clusters are associated closely with developmental genes. That being said, not all of them are clustered near known genic regions, which might be a good indicator that there are heretofore unknown genes in those areas; UCEs might be useful for discovery. And here's a paper trying to give a role to one in cancer.

zoology - Function of carapace

Preface:

1. Any question about adaptation on macro-level has very little meaning and no precise answer.




2. There are two types of larvae in invertebrates: primary ("original") and secondary (evolved from post-larval stages). Not digging into the details, nauplius (together with metanauplius) is the only type of primary larvae in Crustacea and it never has a carapace.




3. "Majority" is by far too strong term, even if we are talking about all larval types. If we just take the largest crustacean orders with species numbers > 1000, together comprising 92% of crustacean species (species numbers are from Ahyong et al, 2011, they seem to be largely correct):

   
   
   
   • Decapoda - 14.7 k species - rarely have nauplius, marine forms do have planktonic carapaced larvae (principally - zoea)
   
   
   • Isopoda - 10.7 k - no carapace
   
   
   • Amphipoda - 9.9 k - no carapace
   
   
   • Podocopida - 6.2 k - no carapace
   
   
   • Harpacticoida - 6.0 k - no carapace
   
   
   • Cyclopoida - 4.2 k - no carapace
   
   
   • Calanoida - 3.1 k - no carapace
   
   
   • Siphonostomatoida - 2.5 k - no carapace
   
   
   • Cumacea - 1.5 k - have carapace, but development is direct
   
   
   • Mysida - 1.2 k - have carapace, but development is direct
   
   
   • Tanaidacea - 1.1 k - have carapace, but development is direct
   
   

So, "majority" could be applied to Decapoda only.

Fabula:

If we substitute "adaptation" with "main biological function" (as you have done) or more correctly "main physiological role":

I would prefer the (a), because carapace does function as a protective structure in those decapod larvae which don't rely on behavioral anti-predatory defenses: see Morgan: "Fishes quickly learned to avoid spined prey, which ... may also increase the rate of evolution of the character". Non-carapaced larvae rely principally on behavior only.

The only contribution of carapace to planktonic life-style in zoea is participation of its spines [when they are pronounced] in parachuting (Chia et al).

[The above should be largely true also for the cypris larva of the cirripeadians, which are enclosed in a non-spined bivalve carapace.]

From the morphological point of view, [at least in adult forms of decapods] carapace creates a chamber for gills, so a morphologist would argue that this is the "main function" of carapace.

biochemistry - Why are omega-3 fatty acids so easily oxidized when they're incorporated in cellular membranes?

I think the explanation for this description of fish oils as "easily oxidised" can be found in the Introduction to the actual paper (Nutrition 27 (2011) 334–337) that is cited in the article linked to in the question.

Fish oil contains high levels of eicosapentaenoic acid (EPA; 20:5 omega-3) and docosahexaenoic acid (DHA; 22:6 omega-3), which are omega-3 polyunsaturated fatty acids. EPA, DHA, and fish oil have been shown to have protective effects against coronary heart disease, thrombosis, inflammatory processes, carcinomatosis, and metabolic syndrome. Therefore, fish oils and components of the oils are marketed as health supplements. However, the effects of omega-3 polyunsaturated fatty acids on aging and lifespan are unclear compared with those of omega-6 polyunsaturated fatty acids contained in safflower oil and soybean oil. EPA and DHA are oxidized easily compared with linoleic acid (18:2 omega-6) and oleic acid (18:1 omega-9) in vitro .

In other words, the fish oil omega-3 fatty acids EPA and DHA have, respectively, 5 and 6 double bonds, whereas the omega-6 fatty acids in safflower oil, linoleic acid and oleic acid have, respectively, just 2 and 1 double bonds. So the fatty acids in fish oil are more prone to oxidation simply because they have so many more double bonds.

Incidentally, as you can see from the two structures below, both of the omega-3 fatty acids, EPA and DHA, also have an omega-6 double bond.

EPA:

DHA:

neuroscience - Is it technically possible to make someone see something when their eyes are closed?

Yes, this is most certainly possible and already being done. As long as the visual cortex of the brain (in the occipital lobe, i.e. at the back of your head) is functional, the correct stimulation will produce visual perception.

In cases of blindness caused by malfunction of the retina, meaning that the rest of the visual pathway is functional, this is the most promising approach to restoring vision. See Visual prosthesis and the TED talk on it.

"Virtual vision" as in projecting a whole field of vision (reflecting the real surroundings) is the big ideal target that this technology is aiming for. Of course as soon as they manage to make a working prosthesis for blind people, someone will probably try to make it non-invasive and easily usable for commercial exploitation.

immunology - Transfer of antibodies in breast milk of humans

It is! Here is an amazing review from 2011 that literally has all the answers. I'm not kidding, all of them. I would marry this review if I could.¹ It also includes information on other animals.

The main takeaway is that IgA from milk is not readily absorbed by the infant body. Secreted IgA is mainly to provide a protective coating for the mucosa while the infant is developing its own nascent immune system. IgG passed along from the placenta (your other question) provides the main source of absorbed antibodies. As it says in the review:

Milk sIgA is not taken up by the infant’s intestinal mucosa. In fact, gut closure in humans occurs before birth and little immunoglobulin is absorbed intact in the intestine after birth. However, the presence of sIgA in the intestinal lumen is part of the protective function of the epithelial barrier in the intestine... Secretory IgA is considered to be the primary immunoglobulin responsible for immune protection of mucosal surfaces such as the intestine.

In terms of enzymatic activity, the digestive system will in indeed chomp up the antibodies; that's part of the reason breast feeding should continue as needed. That's okay, because there's plenty to go around:

Much of the immunoglobulin consumed in an immune milk can be expected to be partially or completely digested, however some portion of the immunoglobulin will remain intact or at least partially intact and capable of binding to an antigen.

It turns out that immunoglobulins are moderately resistant to digestion, at least more so than other milk proteins. There's a section in there detailing some experiments where Ab was given to individuals:

In adult humans consuming a bovine whey protein concentrate, approximately 59% of IgG and IgM was detected by radial immunodiffusion from effluents from the jejunum, while 19% was detected in the ileum. These estimates of digestion of immunoglobulin compare with estimates of digestion of milk proteins in adult humans which are approximately 42% complete at the end of the jejunum and 93% complete by the end of the ileum, again underscoring the relative resistance of immunoglobulins to digestion in the gastrointestinal tract.

Digestive enzymes vary as to which antibody they prefer to digest, but at least some of them will technically digest the antibody, but still leave functional Fab fragments, which are still immunologically active and useful to the infant immune system.

---

_{1: Did I mention I love this review? I love it.}

immunology - Cell identification by Body Cells

Broad question. Summary:

The innate immune system processes everything. When it senses that something is dangerous it tells the adaptive immune system, that is T and B cells, that this thing I'm holding is dangerous (via coreceptors and cytokines).

T and B cells that are specific for this dangerous protein (or sometimes non-protein) are activated.

Ideally T and B cells that react to self proteins are deleted. These are from central tolerance mechanisms when the cells are developing (T and B cells are tested against self proteins; if they react they die) and in the periphery (once they're mature) by them only getting activated by the innate immune system and other mechanisms. There's also T regs which regulate the immune system by preventing any cells that react to self proteins from being activated.

Autoimmune disorders are caused by a break down of these mechanisms.

microbiology - Vigorous shaking for HFR interrupted mating

I remember doing this experiment many years ago in an undergraduate practical where we used vigorous vortexing of culture samples in glass tubes to achieve interruption and separation.

According to Griffiths AJF, Gelbart WM, Miller JH, et al. Modern Genetic Analysis. Bacterial Conjugation:

... sampling is accomplished by using a kitchen blender to separate
the joined cells, resulting in interrupted conjugation.

evolution - Origin of human intelligence and thought

Evolutionary theory is a little over my head, but there are some obvious problems with your question.

We don't descend from any Chimpanzee or Orangutan because, if we did,
they would also have the cognitive thinking ability that we have.

1. We aren't closely related to orangutans, period.




2. The chimpanzee is considered our closest living relative, but that doesn't mean it's a direct ancestor.




3. Why would an ancestor have to have the same cognitive thinking ability we have? Isn't cognition something that evolves?




4. I'm going way out on a limb, but who really knows what kind of cognitive abilities apes have? They probably aren't equal to ours, but still...

I am arguing that a high protein diet allowed the first humans to have
the possibility to develop a higher memory, intelligence and other
mental procedures.

Gorillas are herbivores, and they rank among the most intelligent species. Come to think of it, a lot of people are vegetarians.

But after all, what would be the real origin of the intelligence?

I'm going out on a limb a bit, but I think many scientists associate the evolution of intelligence in humans with a combination of physical traits - particularly binocular vision, bipedalism and our opposable thumb. Walking upright freed our ancestors' hands so they could manipulate objects, stimulating the brain. Note that octopuses - which can similarly manipulate objects with their tentacles - are considered among the most intelligent invertebrates.

If animals do have intelligence too, why isn't theirs as advanced as
us.

Mammals have more complex brains than birds, herptiles and other groups; that gives us a head start.

We're also unique in being completely bipedal AND having opposable thumbs. Which isn't to say only animals with these features can be intelligent; whales may rival us in intelligence. But we obviously have some very unique physical traits.

The human brain is also relatively large and complex - though some might argue that that's a result of our physical characteristics.

biochemistry - Pharmacologically, can tricyclic antidepressants have a side-effect profile similar to neuroleptics?

Torticollis can occur for several reasons, one of which is a side effect of certain drugs. Rather than highlight one specific drug it is perhaps better to talk about the mechanism of action by which this occurs.

Torticollis in a drug induced form is classed as an extrapyramidial side effect. Classically results from some medications which have anti-dopaminergic effects. The neurotransmitter dopamine is important for the regulation of movement. Different medications have different degrees of anti-dopaminergic effect. To complicate things further there are several different types of dopamine receptors and different drugs have different effects depending on their action on these receptors.

Classically drugs that have been associated with extrapyramidial side effects are some of the antipsychotics but there are case reports of this with trycyclics http://www.ncbi.nlm.nih.gov/pmc/articles/PMC489096/ however this appears to be a very rare, see http://www.sciencedirect.com/science/article/pii/S0924977X97004057.

The paradoxical treatment of torticollis might be dependent on the cause of the condition. Tricyclic anti-depressants have anti-cholinergic effects, i.e. they block the effects of the neurotransmitter acetylcholine. This neurotransmitter works in opposition to dopamine in the basal ganglia (part of the brain responsible for movement control) as such might be used when the dystonia is as a result of doperminergic disregulation.

If you are at all concerned that you may be suffering side effects of any medication, then I highly recommend that you go and discuss this matter with your doctor. The above is a simplified explanation of some of the reasons why these side effects may occur. It is not intended as information for the purposes of self diagnosis and treatment.

pharmacology - How does paracetamol interfere with immune system?

First question: Yes. The immune system releases pyrogenic cytokines such as IL-1. Bacteria aren't typically used to 37C, they prefer working at under that temperature to function in the environment. Our body however can take a few degrees here or there however this severely compromises the bacterial enzyme activity. The same is true for other pathogen enzymes. The body also increases copper concentrations in the blood for similar reasons. Problem is of course if the body goes into overdrive and raises our temperature too much, this compromises our own ability to fight the infection so in that case antipyretics like paracetamol can reduce fever.

Second question. It isn't a side effect, however paracetamol works by blocking things like IL-1 that raise temperature. How IL-1 raises your temperature is quite interesting, it tells the hypothalamus (our thermostat) that it should be set higher. So we feel cold (so we try to keep ourselves warm) and the body thinks it's cold (so it increases the temperature by burning glucose mainly)

evolution - What does "fit" mean in "survival of the fittest"?

'Survival of the fittest' has never really made sense, because it confuses the scientific (evo. biological) and colloquial definitions of the word - which some of the previous posters have also done.

Biological fitness simply refers to an individuals genetic contribution to the following generation. That is, a 'fitter' individual, in an evolutionary sense, is one whose genetic material is proportionally overrepresented in the next generation.

The mechanism by which an individual achieves this may include out-surviving competitors, but it's certainly not the only way to increase fitness. Two individuals may live for the same length of time, but one may successfully court more females, or out-compete the other for food resources, for example. So when we refer to a 'fitter' individual (or individuals), we're saying nothing about why they are so. It's not a comment on their 'fitness' in the human sense of the word (bigger, stronger, longer-living), it simply refers to how well they pass on their genetic material.

So you can see why the phrase is nonsense. If we're being precise, then 'survival of the fittest' translates to 'survival of the individual who is better able to pass on their genetic material to the next generation' - which is meaningless because it tangles up these different concepts.

evolution - Why are some fungi poisonous?

The same reason some plants are poisonous: to stop animals from eating them.

The visible part of the fungus is called, rather misleadingly, the fruiting body. It exists to produce and spread spores and thus produce the next fungal generation. Getting eaten, rather obviously, inhibits its ability to do this. Being poisonous discourages animals from eating the fruiting body and thus permits it to complete its life cycle.

physiology - Which is the tissue damaging agent in krokodil (street desomorphine)

Note: Don't click on the links, or even search for information, if you don't have a strong stomach

From what I've read, it's not necessarily 100% known, most likely because it's not easy to study (small, reclusive users who die quickly of a complex concoction) but the line everyone has quoted is:

"They extract [the drug] and even though they believe that most of the oil and gasoline is gone, there is still remnants of it. You can imagine just injecting a little bit of it into your veins can cause a lot of damage… it eats you from the inside out".

That's from Dr. Frank LoVecchio in Phoenix, Arizona, who saw two cases within a week. It's not hugely scientific, but it's not wrong. Krokodil is never pure and highly toxic chemicals are thus injected into the veins. If you want specifics, then gasoline, hydrochloric acid, phosphorous scraped off matchboxes, paint thinner, iodine, and cleaning oils. Injecting any one of those should be enough to kill a repeated user. Those substances rupture blood vessels, and the subsequent leakage creates gangrenous wounds like you see in the pictures.

biochemistry - Simple diffusion of lipid-soluble molecules through phospholipid bilayer -- does anything get "stuck" in transit?

I think, given Alan's answer the question you might be asking is something like
'do compounds become concentrated in the lipid bilayer', as opposed to achieving high concentration inside the cell after diffusing through the membrane as he describes.

This could certainly happen (if that's what you're thinking), but usually won't for I think two reasons.

The first is that any molecule that would not soluble in the interior of the cell is going to have a correspondingly small not going to be found in the blood or lymph, tissue, ocean or other milieu the cell is living in, which will be mostly water.

You might well ask whether there are cases where the compounds in question might be available in low concentrations around the cell and over time accumulate in the lipid bilayer. This slow concentration model probably happens, but there is a compensating mechanism - the lipid bilayer is taken into vescicles and degraded, to be replaced by newly synthesized such that membrane components renew themselves. This process includes the cell engulfing by endocytosis and specifically turning over membrane proteins.

The turnover rate for most cells is on the order of days, some of the best numbers for this are behind a paywall, but a reference to synaptic membrane turnover shows some components turn over varying between 6 and 24 days. Different components such as cholesterol, phosphatidylcholine and phosphatidylethanolamine have differing rates of turnover.

So between these two effects, the concentration of 'permeant molecules' would be low for most cases.

biochemistry - What Biology topics are linked to the Nitrogen Cycle?

The nitrogen cycle is a highly biological process. Nitrogen gas is ~75% of the earth's atmosphere and N₂ is the most chemically stable form of Nitrogen for conditions in the Earth's crust.

Nitrogen is one of the four most essential and universal elements to terrestrial life (Carbon Hydrogen and Oxygen being the others). Nitrogen fixation, the name given to the various processes which make chemically reactive forms of Nitrogen available to living things. Ammonia (NH₃ / NH₄⁺) and Nitrites / Nitrates (NO₂^-, NO₃^-) are chemically unstable compared to N₂ and the conventional biosynthetic processes in the cell can use any of these forms to make proteins, nucleic acids and other biologically active molecules necessary for life.

Ammonia and similar compounds like Urea come from the biological byproducts of living cells - waste. These are readily recycled in the soil by plants and microorganisms and I imagine some animals and insects. Nitrogen is a limiting resource for living things and most biomes are pretty efficient at recycling reduced nitrogen from primary (NH₃) secondary (NHR₂), tertiary (NR₃) and quaternary amines (NR₄).

But the biosphere has a great demand for bio-useful nitrogen and in most places on earth in deep water and soil microorganisms can break down N₂ directly into nitrates/nitrites. This happens deep underwater or underground because the enzymes which perform this activity are delicate and ruined by O₂. This process is entirely performed by anaerobic microorganisms. In recent decades, the ecological importance of subterranean microbial communities has become better appreciated for the complex structure and ecological roles it plays.

An interesting side note to this is that up to the early 20th century, the growth of life and human civilization was really limited by the intense labor required to grow food. While hydrogen oxygen and carbon are essentially free - obtained from water, atmospheric oxygen and CO₂ by plants, Nitrogen was the limiting factor in many cases to growing more crops or animals for food.

The Haber process, which converts nitrogen and hydrogen gas under high temperature and pressure into ammonia over a catalyst was such an important discovery - it allowed the industrial preparation of effective fertilizers and was instrumental in creation of the green revolution.