Did baby bird hair and mammalian hair convergently evolve? Chicks (baby of chickens) and ducklings seem to have fine hairs, at least something that look like hairs to me. Most mammals have hairs, but reptiles, fish, or other animal groups do not have hairs as far as I know.

I have looked up the tree of evolution, and it looks like this.

So, the tortoises, crocodiles (I do not know what lepidosauria means but I guess it is reptiles other than the aforementioned), and birds diverged after their common ancestor was split from the common ancestor of mammals.

Since none of the tortoises, lepidosauria, or crocodiles have hairs now, does this mean that the hair of birds and mammalian hair is an example of convergent evolution? Or did these other taxa lose hair during evolution?

Bird "baby hair" are modified feathers.  (Or perhaps feathers are modified "baby hair".  The ancestral state for feathers was probably closer to the chick's down in appearance, but I don't know whether chick down is unmodified original feather or whether it was feathers and then modified again.)

In any case, mammalian hair and dinosaur feathers (which includes bird feathers) are separately evolved from the same base structure, modified reptilian scales. They are therefore homologous, but evolved independently.

  These results reveal a new evolutionary scenario where hairs, feathers, and scales of extant species are homologous structures inherited, with modification, from their shared reptilian ancestor’s skin appendages already characterized by an anatomical placode and associated signaling molecules.

--The anatomical placode in reptile scale morphogenesis indicates shared ancestry among skin appendages in amniotes


Ill effects of urea and NH₃ on metabolism What exactly does urea do that harms our body? Does it interfere with our cellular processes or disturbs the colloidal onchotic pressure of our blood?
I have heard that NH3 damages the brain. What does it actually do?

The denaturing effect of Urea is mostly at very high concentrations.   (~Molar levels)!

Physiologically, urea, a product of the breakdown of retired amino acids, will build up rather quickly if it weren't secreted in the urine. Looking into this, it doesn't seem as there is a clear understanding of why this causes a disease, though the buildup of a waste product definitely is a unifying concept.

Uremia - kidney failure - causes a build up of urea in the blood as the kidney eliminates urea from the blood into the bladder.  The specific effects of Urea on cell metabolism are probably numerous as the symptoms:  anorexia and lethargy, and late symptoms can include decreased mental acuity and coma. Other symptoms include fatigue, nausea, vomiting, cold, bone pain, itch, shortness of breath, and seizures.

Being a metabolic waste product, it certainly would interfere with and inhibit any enzyme that produced urea - the Urea cycle in particular.  Its clear that uremia is ultimately associated with cell death, oxidative stress, some cell signalling and proliferation.

I'm just googling around here, but I don't think there is any one single answer as to what goes wrong when the cells are exposed to too much urea.


To understand clearly extraintestinal diseases Extradistestinal disease seems to prefer to "bowel" diseases, I think this is about diseases outside gastrointestinal tract so stomach.

Consider diseases ulcerative colitis and Crohn's disease (enteritis) as examples.
Colitis affects to colon, outside of small intestine, I think extraintestinal therefore.
Crohn's disease (enteritis) however affects to the small intestine so I would think intestinal disease (but this clause is wrong) - it should be at least have extraintestinal manifestations.

What is the exact definition of the word extra in intestinal diseases?

Certain intestinal diseases have symptoms that appear concurrently in other systems of the body, but the bowel diseases themselves are not extraintestinal.

  Extraintestinal manifestations of inflammatory bowel disease are prevalent in both ulcerative colitis and Crohn's disease. The most common manifestations involve the musculoskeletal and dermatologic systems. Other manifestations involve the hepatopan-creatobiliary system (eg, primary sclerosing cholangitis) as well as the ocular, renal, and pulmonary systems1.

One of the key differences between extraintestinal manifestations and comorbid conditions (though seemingly not a necessity, the article cites primary sclerosing cholangitis as an counterexample) is that the extraintestinal effects will subside once the disease of the bowel is treated.

1 Levine, J.S., Burakoff, R. (2011). Extraintestinal Manifestations of Inflammatory Bowel Disease. Gastroenterol Hepatol (NY), 7(4), 235–241.


How do detergents interfere with protein assays? This has been getting me stuck. I've tried to understand what a detergent would do in an assay, but I can't figure out whether it would affect the protein or the reagent (say, in a Bradford assay).

Depending on the detergent, its concentration, and the exact assay being performed, it can affect both the protein and the assay reagent(s). Some detergents will bind the (usually colorimetric) reagent, or otherwise chemically react with it, giving high background to your assay and sometimes completely masking the specific signal of the assay itself. Many modern protein assays are tolerant of a fairly low level of various detergents, perhaps some but not others, and this underscores the necessity of running a buffer/diluent-only control to verify the background of your measurements. Other assays, like Bio-Rad's DC Protein Assay or the Pierce Detergent Compatible Bradford Assay Kit from ThermoFisher, are engineered to tolerate a certain (often fairly high) level of detergent without increasing the background of the assay.


What kind of worm is this? What kind of worm is this? I’ve seen them in my bathroom and kitchen which are both ceramic tile. This morning I walked in the kitchen and this one just so happened to be dead.

I'd say that isnt a worm but a nonvenomous blind snake specie named Indotyphlops braminus
(Indotyphlops braminus)  .(Brahminy Worm Snake )


What are "+" and "Ar" in consensus binding sequence of amino acids? So I was reading this paper and found a figure as below:

I understand that [LEAM] means any of LEAM residues, pS is phosphoserine and X means any amino acid residue.

What is [+] here ? Is both R and Ar arginine itself?

Ar means aromatic and + means positively charged residues. However, this is not a standard code (as of now).

From the same paper:

  Sequences closely matching these optimal binding motifs, R-X-[Ar/S]-[+]-pS-[LEAM]-P and R-[S/Ar]-[+]-pS-[LEAM]-P, denoted as mode 1 and mode 2 consensus sequences, were found to be present in many known 14-3-3 ligands ( Yaffe et al. 1997), where Ar denotes aromatic residues and + denotes basic residues.


Can somebody identify this species of spider? I ran into this cool looking spider in my yard in Banjaluka, Bosnia and Herzegovina.  It's about the size of a fingernail and unusually shaped (spherical). Could it be poisonous?

The white cross on the body makes me think it could well be an Araneus diadematus. It is quite common and not dangerous for humans. It paralyzes its preys using some venom, though.


Book on the history of Darwin's discoveries and development of his theory This question is a book request. I am wondering if there are any books with these elements:

Tells the history of Darwin's discoveries.
Captures Darwin's changing views of the origins of species, because of his discoveries and his thinking on the subject.
Is a modern text but incorporates some of Darwin's writings (e.g. from the Voyage of the Beagle, etc).

Note: I am not asking for a book that is just explaining the process of natural selection, rather I am looking for a historical book about Darwin's discoveries and the inception and development  and eventually his publication of his theory of natural selection.

I'm not certain it fills every element of your question, but I really enjoyed Michael Ruse's "The Darwinian Revolution: Science Red in Tooth and Claw."

It's especially good for setting up the collection of worldviews that predated Darwin, and the influence on him by both biologists/anatomists as well as very crucially geologists like Charles Lyell (Darwin really thought of himself more as a geologist; the long time prior to publishing Origin was largely because he was trying to build up some scientific chops as a biologist).

The aspect it is most likely to lack is references to original source material from Darwin. While it certainly draws on such writings, I don't recall it actually containing reproductions of those writings, at least not on a substantial basis.

Importantly, however, this book is not a biography - it is a history of the scientific community at the time, centered around Darwin and Origin and placing them in relevant context.


Lineage selection in plasmid evolution I've been reading through Paulsson (2002) and I am not sure what he means by "lineage selection" in the second to last section. The paper deals with plasmid replication, and mostly concentrates on the contrasting pressures from two levels of selection:

intracell selection - competition between plasmids in a single cell. A plasmid can undergo a cis-mutation and over-replicate, resulting in a higher intracell fitness than the focal plasmid. The plasmids reproduce.
intercell selection - competition between cells. Cells with a heavier load of plasmids will take longer to reproduce, and plasmids that produce a heavy load will have lower intercell fitness. The cells containing plasmids reproduce.

In this context, what does the third level of selection -- lineage selection -- mean? What reproduces? How do the lineages split or interact?
My guess
Does lineage selection simply mean group-selection on separate colonies of cells? In that case, how are new lineages formed? I would expect this group level to select for zero levels of plasmids (since they place no loads on the cells and thus these groups of cells will grow the fastest), but Paulsson (2002) suggests the opposite:

lineage selection could favor plasmid traits that help the population of plasmid-containing cells to fight plasmid-free cells.

Is there a more detailed discussions of this available than the one section in Paulsson (2002)? Neither the unit of selection nor either the evolutionary or genetic lineage Wikipedia articles address my question. The first only mentions lineage in passing, and the second two don't discuss models of selection.

References
Paulsson, J. (2002). Multileveled selection on plasmid replication. Genetics, 161(4): 1373-1384.

He defines lineage selection as selection for traits which increase the fitness of a group of plasmids, rather than an individual plasmid with in a cell or a particular cell containing plasmids. He says that the unit of selection are "plasmid-host clades" : in other words the unit of selection is the group of closely related plasmids in separate cells. It is an example of a kin-selection though I haven't seen the specific terminology in widespread use. He likely doesn't use kin selection because the plasmids don't have well defined offspring, so he uses a broader term for kin--lineage. I might have preferred clade selection, but this term has its own baggage. I'm not sure (and neither is Paulsson) that kin selection is need to explain 'spitefully low loss' rates, since intra-cellular and inter-cellular selection both favor lower loss rates.


Is NMDA produced in the body? On the wiki page for NMDA it says that NMDA is a synthetic substance that mimics glutamate. So why does the body not use glutamate instead of NMDA?

Also how is it possible that our body can produce something that is synthetic? I thought synthetic was man-made chemicals. Does that mean the NMDA receptors it binds to are also synthetic? How did this come to be?

(my comment reiterating the answer seemed useful, so I've reproduced it here)

There are "NMDA receptors" in our body. There is not NMDA naturally in our body*. "NMDA receptor" is just a name people gave to one of the receptors that normally binds glutamate. They could have called it something else, like the "slow glu receptor", or "Glutamate Receptor A", but they called it the NMDA receptor because they discovered it was different from other glutamate receptors in that it was activated by a chemical called NMDA in their experiments.

(original answer)

NMDA receptors are in fact glutamate receptors natively: there is no endogenous NMDA*. They are named NMDA receptors because experimentally they were differentiated from other glutamate receptors using the compound NMDA. At first glutamate receptors were known as "NMDA" and "non-NMDA" glutamate receptors, and later the non-NMDA sort were found to be sensitive to AMPA or kainate and named thusly.

Many other receptors are named this way: the nicotinic acetylcholine receptor is the receptor that nicotine is an agonist at, but the endogenous ligand is acetylcholine; muscarine is an agonist to the muscarinic acetylcholine receptor but the endogenous ligand is acetylcholine.

Watkins, J. C., & Jane, D. E. (2006). The glutamate story. British journal of pharmacology, 147(S1), S100-S108.

*In the comments, @gilleain pointed out some research suggesting that NMDA does exist endogenously, although in fairly specific areas and not disputing that glutamate is the primary endogenous agonist for NMDA receptors. This work was long after the NMDA-sensitive glutamate receptor was discovered and named, but is some interesting trivia nonetheless.


Text Book Recommendation: Organic Evolution I was wondering if anyone could point me in the direction of any text books on organic evolution? I have recently become interested in the subject and would like to know more. I think an undergrad level book would be a good place to start, but if you would like to recommend any graduate level books it could also be helpful.

I have a background in mathematics and modeling using mathematics. I have also taken a genetics class and an intro to cell biology class as well as read some papers on both subjects. Any help would be nice.

update

I was looking for a higher level discussion on the mechanisms of evolution. A better term to use might be evolutionary biology.

Sorry for the confusion I was under the impression that "organic evolution" was a common term.

Thank you for your time.

Organic Evolution - Definition

'Organic evolution' was a common term. It is just rarely used today. Today, we just say 'evolution' or 'evolutionary biology' when referring to the field of study of 'evolution' (or of study of 'evolutionary processes').

Book recommendation

Math oriented

As you are used to work in applied mathematics, you'll definitely be interested in an intro book to population / evolutionary genetics. Population genetics is the mathematical basis of evolutionary theory. You will find recommendations at the post Books on population or evolutionary genetics?.

For you, I'd recommend Population Genetics: A Concise Guide as a start (or another one presented in the first section of the top answer to the post I referred to above). If then, you like coalescent theory (branching process), you might want to look at Coalescent Theory: an Introduction or some other more specialized books.

Not Math Oriented

Maybe you'll want something more introductory with much less math such as the Evolution: Making sense of life by Zimmer and Emlen or Evolution by Futuyma. These books are classic textbooks for intro class to evolutionary biology in Bachelor. These books will have the advantage to present you some other subfields of evolutionary biology such as the diversity of life, reading phylogenetic trees, ecological relationships and many other things that the books of population genetics don't go over.

Most common fields of math used in evolutionary biology

The most common fields of mathematics used in evolutionary biology are system dynamics, game theory, approximation theory, probability theory, branching processes and diffusion equations.


Does conjugation support gene selection? I have already posted this on chat but haven't got any response. A recent question on group selection stimulated me to ask this here.

QUESTIONS: Why should bacteria conjugate? If we consider that a bacterium is another bacterium's rival (in terms of obtaining resources) why should a bacterium "share" it's antibiotic resistance gene, for example, with another bacterium? I can think of 2 reasons. One is group selection, and the other is "Gene Selection". Group selection has been highly criticized in recent years, and individual selection has dominated thinking, but here my support goes for gene selection rather than individual selection.

Gene selection seems to me the easier explanation over individual selection. Even if we consider the fact that a colony is made from divisions of single cells and the cells are extremely similar and also that conjugation is more probable between cells of a colony, we should also consider that conjugation can happen between very different bacterial species.

Interesting Question (glad the "group selection" post got you thinking!)

Me and two friends thought about your question during our Biology BSc at ICL (in fact we also thought about an even more puzzling phenomenon called "bacterial transformation" which is like conjugation, but they incorporate genes from dead bacteria!!) our first year course convener recognized our answers as "most likely candidates" so here they are:

1. Stress-induced Experimentation Hypothesis

The likelihood of conjugation/transformation occurring may change for a bacterial population as a whole depending on how stressed it is (or perhaps how unfamiliar the environment is?). Stress signals could cause the population to be more "risky" and take up the DNA from surrounding living/dead bacteria and incorporate it with its own genome: "the hell, we're out of options.. lets transform into something that resembles the indigenous species of this strange ecosystem!". Indeed Bacteria have memory (see: chemotaxis) this means that perhaps they can be able to tell whether they have been receiving more stress now as opposed to before, meaning they can "trial and error" with various genes that have been imported within their plasmids! — "Let's try this gene, oh wait... I'm dying, hmm let's kill off this plasmid and take some more genes!".

In reply to this my course convener said:

  "ah yes, a switch from asexual to sexual reproduction occurs in
  many organisms under stress. The genes that cause the
  sex/transformation to occur may gain a net benefit from recombination
  with genes taken from other organisms/the environment."

2. Diversity Plagarism Hypothesis

If we look at the entire population of conjugating bacteria as a single competitive unit itself (e.g. like a tissue is a coordinated group of specialized cells) that can compete with other populations of bacteria who cannot conjugate the conjugating population will "win". This is because a conjugating population will always have much higher phenotypical diversity as it can mix traits between the individuals. This means a conjugating population is much more efficient at undergoing natural selection for beneficial traits or trait combinations.

Think of natural selection (coupled with mutation) as an inventor... something that helps you invent much "fitter bacteria" is the ability to pull things apart from this bacterium and that bacterium and glue them together, this is essentially what conjugation/transformation does!! it allows you to pull bits from this bacterium and stick it to bits from that bacterium to get a "super-bacterium". It's like open source technology (free to share) as opposed to patented technology!! Conjugation is immediately a good thing because it means you can "steal" cool technology from living/dead bacteria and incorporate it into your population's gene pool!

Hope this was helpful!


What is in the space between neurons in a brain? When neuron animations are displayed, there are frequently seen neurons, axons arranged in a lattice with a lot of empty space between. I'm interested if there is indeed empty space in the brain, or if it is filled with some sort of fluid? I've checked an article on cerebrospinal fluid but am not sure that it is present all throughout the brain.

The reason I'm asking is that I'm thinking of neurotransmitters- they are released in synapses, but I'm not sure how they stay there - are they suspended in some liquid as well?

Not so empty, actually.

The human brain has a mass of ~1.5kg, and volume ~1200cc (a little bigger for men, a little smaller for women). So is heavier than water by a good margin.

While it has Cerebrospinal fluid, that only occupies the subarachnoid space (the space below the skull and above the cortex, contained between two layers: pia matter and arachnoid membrane) and the ventricular system (several spaces inside the brain, remnants of the embryological development of the brain).

Neuron density may vary widely, depending mainly on the particular characteristics of neuron cell types and their interconnections. But besides neurons, there's a lot of infrastructure inside the brain. For example:

Astroglia: They are a type of glial cells which participate in the formation of the blood-brain barrier (supporting the endothelial cells), nourishing of neurons, maintenance of ion and neurotransmitter concentrations, among others. They also keep in place most of the tissue.
Microglia: Small cells with immune (phagocitic) functions inside the brain.
Radial glia: A more specialized precursor cell, that also participates in neuronal migration in the brain.
Oligodendrocites: Cells responsible for the insulation (myelination) of axons.
Neuroepithelial cells: The stem cells in the brain.

Neuroglia, which includes the first four cell types above, accounts for ~90% of tissue in human brain (http://classes.biology.ucsd.edu/bipn140.WI13/documents/Gliamorethanjustbrainglue.pdf).

Also, when you collect some billions of axons, they can be quite representative in terms of mass and volume. The ratio between white matter and gray matter is close to one for humans, but lower for smaller mammals (http://www.pnas.org/content/97/10/5621.full.pdf).

About the last part of your question, the synaptic cleft (the space between pre-synaptic and post-synaptic neurons) is a salty solution: water with high concentration of sodium and chloride ions (and also calcium ions, neurotransmitters and a lot more). These ion concentrations are fundamental to the generation of action potentials, neural signaling, and the general dynamics of the brain.


Is there a way tell apart dinosaurs from similar extinct reptiles? When I was a child, I thought I knew what a dinosaur was. But, as I grew older, I was told that many of the extinct species that I thought were dinosaurs (dimetrodons, pterosaurs, plesiosaurs, etc.) were not in fact dinosaurs. Is there a reasonably quick way for a lay person to tell apart true dinosaurs from non-dinosaurs without taking up an in-depth, species-by-species study of paleontology?

There are several defining morphological characteristics of dinosaurs. Including their ankle structure and perforated acetabulum, Aka the hole in their hip goes all the way through, as well as a few other minor features. These combined makes it literally impossibly for a dinosaur to take on a sprawling pose without breaking hind leg in many places, this is why you will often see an erect posture given as the reason, but that is a product of these feature not the defining feature itself, there are many ways to achieve upright posture.

Now of course we are moving away from purely morphological definitions, cladistically dinosaurs are defined as The last (most recent) common ancestor of Triceratops horridus and Passer domesticus (common pigeon), and sometimes Diplodocus carnegii as a third, and all of its(the ancestor's) descendants.

A more superficial quick and dirty method is if it is a pterosaur or lives in the ocean it is not a dinosaur, If its limbs sprawl it is also not a dinosaur. I should also include this guys work, since he attempted to create a complete cladogram of every dinosaur, so you can visualize the group.


3 fates of this matter When an animal eats something, it obtains matter and energy right? But, what are the 3 possible fates of the matter and 3 possible fates energy. I don't understand what they are even asking. What would be the 3 possible fates of each.

I think the poster wants only a simple answer, so I am going to answer in simple terms. The fates can be -

1 Used in cellular respiration as fuel and some amount can be converted to useful energy which can be used to build other substances and some energy can be lost as heat.

2.The animal can become prey for other animal.

3.The animal throws away some matter as feces.


Can we estimate effective population size from DNA sequence data (CR or cytB sequence)? I have DNA sequence data (control region) of two population of a species. Can anybody suggest me any software to calculate effective population size? Is it possible and meaningful?

It sure is possible.

Very simple model

It is often hard to decompose the effective population size $Ne$ from the mutation rate $\mu$ though. But it is quite common to estimate $N\mu$. For example, it is a classical result from coalescent theory assuming a single panmictic population of constant size and no selection (and a few other assumptions) that

$$N\mu = \frac{S}{\sum_{i=0}^{k-1} \frac{1}{i}}$$

, where $S$ is the number of segregating sites and $k$ is the number of sampled individuals.

More advanced models

You will probably want a slightly more advance model though.

There exist a number of estimators including Colony2, CoNe, Estim, MLNe, ONeSAMP, TMVP and LDNe. I recommend having a look at Gilbert and Whitlock (2015) who compares these estimators under different demographic scenario.


Do low light levels during development affect the distribution of rods and cones in the retina? I just can't seem to find any retinal development experiments that have been done using low light conditions. I am very interested in knowing if raising an animal in such conditions leads to a different distribution of rods and cones in the retina. Perhaps it would lead to a more uniform distribution that the skewed distribution that is normally found?

Any thoughts or pointers to resources would be appreciated!

I found a few studies in fish that showed constant light exposure changing rod density. First one in goldfish:

Raymond PA, Bassi CJ, Powers MK.
Lighting conditions and retinal development in goldfish: photoreceptor number and structure.
Invest Ophthalmol Vis Sci. 1988 Jan;29(1):27-36.
http://www.ncbi.nlm.nih.gov/pubmed/3335431

  The retinas of 63 goldfish were examined after varying durations of exposure to one of three environmental lighting conditions beginning before hatching: constant light (340 lux), cyclic light (12 hr 320 lux, 12 hr dark) and constant dark. Up to 8 months, no effects of constant light or dark on photoreceptor numbers or structure were apparent. Densities of rod and cone nuclei were normal and all retinal layers appeared normal by light microscopy. Exposure to constant light for 12 months or longer resulted in a reduction in rod density by 37%. Cone numbers were unaffected by constant light, even with exposures of 3 yr, and rod and cone outer segments were normal in length at 11-20 months under all environmental conditions. Due to poor survival, only one animal was available for quantitative examination from the group reared in constant dark 12 months or longer. Photoreceptor size and number in this retina were similar to those in the constant light condition. The results suggest that the formation and maturation of rods and cones in goldfish retina is unaffected by rearing in constant light. However, long-term exposure (greater than or equal to 12 months) may disrupt maintenance of differentiated rods.

See also http://www.vision-in-cichlids.com/fenotypic_plasticity.htm where they say rod density changes in early retina development of Tilapia leucosticta.


What is a "segregating gene"? What does the term "segregating" mean in references like the following:

"found 42% of a random sample of loci to be segregating"
"15 blood group systems are known to be segregating"

If, at a locus, you have several alleles, then this locus is said to be polymorphic or segregating.

A segregating locus is just an untintuitve name for a polymorphic locus.


Why are diabetic people often overweight? I was looking at diabetes the other day, and I noticed something strange. Lower amounts of lipase are a symptom of diabetes, as is overweightness. However, since lipase is the enzyme that breaks down fats, shouldn't a lack of it mean that less of it enters your blood stream and is simply excreted instead? In that case, how come diabetic people are often overweight?

This question has been bugging me for ages, does anyone know why?

How are diabetes and obesity connected in light of low lipase activity?
Short answer: There's more than one type of diabetes.  (And to complicate things, there's also more than one type of lipase.  It's unclear from the question which type were mentioned in what you read.)

Diabetes mellitus is usually divided into Type 1 (insulin-deficient) and Type 2 (insulin-resistant).  Obesity is a risk factor for Type 2 diabetes, but not all diabetics are overweight. In fact, people with Type 1 are often lean.

Decreased lipase activity is not a major symptom of diabetes.  However, these two articles suggest that plasma lipase activity may be lower in cases of Type 1 diabetes but not Type 2.
Junglee, D. et al., Low pancreatic lipase in insulin-dependent diabetics, 1983.
Dendona, P. et al., Exocrine pancreatic function in diabetes mellitus, 1984.


Why are proteins always made in N to C direction? Why are proteins always synthesized from the N-terminus to the C-terminus? Can there be any “reverse” peptide-bond formation to synthesize proteins in the C-terminal to the N-terminal direction?

Nice question! As you already know, DNA is always shown in 5'$\rightarrow$3' direction because it is always synthesized in this direction (amino acids are joined by CO-NH peptide bond). So, a polypeptide looks like this (source):

In fact, if you just look at the polypeptide in the reverse direction, you could view it in C terminus to N terminus direction. But we don't do so because that is not the conventional direction of the polypeptide's biosynthesis.

Tracing the Roots: To know why there is no "reverse" peptide bond (NH-CO), we first need to know how peptide bonds are formed in polypeptides. Polypeptides are formed in ribosome, and the process of formation of peptide bond occurs in the peptidyl transferase complex of ribosome. Since ribosome is a ribozyme, this reaction is also catalyzed by the catalytic sites of RNA (i.e. 2'-OH) instead of proteins. See the image below for the mechanism (from Marina V. Rodina):

As visible from the diagram, nitrogen (in -NH2) from acceptor tRNA (A site) attacks the ester linkage at the peptidyl tRNA (P site). Carboxylic carbon cannot attack the nitrogen (for "reverse" bond formation) because it is already in ester linkage. One might ask then "if the nitrogen was joined to tRNA at P-site, the carboxylic carbon could have attacked on amino acid at A-site. Why is amino acid not joined to tRNA by the amine nitrogen?" To know why it is so, lets go a step further and see how tRNAs are charged i.e. how aminoacyl tRNA synthetase works. Aminoacyl tRNA synthetase charges tRNA in a two-step reaction. For displaying mechanism, I will take the example of histidyl-tRNA synthetase (diagrams from Proteopedia):

amino acid + ATP → aminoacyl-AMP + PPi

→
aminoacyl-AMP + tRNA → aminoacyl-tRNA + AMP

As is clearly visible now, whether amine nitrogen or carboxylic carbon will attach to phosphate of ATP is decided in the first step. See the image again:

You might ask that since nitrogen (in -NH2) also has a lone pair of electrons, it could also make a nucleophilic attack on the phosphate group, similar to the oxygen (in -COOH). Why doesn't this happen then? This cannot be accounted for by saying that the amine nitrogen is far away from the reaction site (look at the diagram again, and pay attention to how close the carboxylic carbon and amine nitrogen are. If we could move the amino acid even a little bit, this reaction could easily occur). Well, here's the twist: the optimum pH of this reaction lies near pH 6 i.e. in the acidic pH range (Lui et al, 1978). Now, as we know, under acidic pH, -NH2 exists in the protonated form i.e. -NH3+. In this condition, nitrogen lacks lone pair and thus cannot attack phosphate on ATP. Thus, it is not possible to attach amino acid to AMP via -NH2 group and, thus, form a "reverse" peptide bond. I hope this depth of the answer would be enough to satisfy your curiosity :)


Infection treatment without anti-biotic When we have some bacterial infection, say throat infection (pharyngitis) we take antibiotics as treatment. I was wondering how throat infection was treated when there was no antibiotics at all, before 1940's I think.

Throat infection is just example, It can be post surgical operation, urinary track infection etc, basically anything where we use antibiotics currently. So in a way replacement of antibiotic tablet when antibiotic wasn't available.

Interestingly, treatment of mild pharyngitis before the advent of antibiotics wasn't too different from what it is today - it was (and still is) mostly symptomatic. First of all, viral pharyngitis, which is quite common (Hidreth et al., 2015), is not affected by antibiotics (no viral infection is), and they are not indicated in such situations. Second, mild and self-limiting bacterial infections, including pharyngitis, most often do not warrant prescription of antibiotics, as this leads to the growing problem of antibiotic resistance, which, according to the World Health Organization is "one of the biggest threats to global health." Many guidelines can be quoted, urging clinicians to prescribe antibiotics sparingly, but pharyngitis is so common (literally everyone has had it, multiple times) that one can simply turn to one's own experience - simply put, when you have a mild case of soar throat, your doctor doesn't give you antibiotics (if you even bother going to the doctor about it), most often you are advised to take only symptomatic medications (many of which are OTC). These most often include compounds with analgesic, antiseptic, and/or anti-inflammatory properties. Interestingly, such compounds were widely available long before the advent of antibiotics and even the pharmaceutical industry itself.

Menthol, for example, is a selective agonist of κ-opioid (Galeotti et al., 2002) and a modulator of GABBAa receptors (Watt et al., 2008), thereby eliciting analgesic and anaesthetic effects, respectively. Moreover, by disrupting bacterial cell membranes, menthol (and similar compounds, such as thymol, for example), elicit antibacterial activity, as well (Trombetta et al., 2005). Thus, wild mint, peppermint, and thyme are much more often indicated in cases of soar throat than antibiotics! Their use in the form of infusions and decoctions likely predates most, if not all, modern countries. Moreover, the analgesic and anti-inflammatory properties of willow bark, which are due to the salicylic acid contained therein, were known to Hippocrates (Norn et al., 2009), quite possibly dating back much earlier. Furthermore, it is known that caffeine potentiates the analgesic effects of many nonsteroidal anti-inflammatory drugs, including salicilic acid (Granados-Soto and Castañeda-Hernández, 1999). Unsurprisingly, this combination is often found in many modern drugs (many OTC), being marketed all over the world. Whether this effect was known before the advent of the pharma industry, however, is hard to say. Willow bark has been used as an analgesic and anti-inflammatory medication since ancient times, but coffee was brought to the West in the XVI century.

This is only a handful of traditional medications for pharyngitis, and I'm sure many more can be found, as well as many other treatments for many other conditions. The point is that treatments of mild pharyngitis were available before the advent of antibiotics, as a matter of fact, many of those treatments are still first-line therapy in most cases, even to this day.


Does the human body convert water? I just read Andy Weir's "The Martian" (which was very good) and one line made me wonder:

  [...] a human body only borrows water.

Is that true? Does all water "that goes in, go out"?

Yes, the human body "converts" water.

Out of the hundreds of chemical reactions going on in the human body, there are reactions which take water as an input and "react it away" into something else. There are also reactions which create water out of other molecules.

Example 1: Hydrolase reactions. They have the form of

  A–B + H2O → A–OH + B–H

You get water as input, and something else as output.

Example 2: Peroxidases "defuse" the highly reactive hydrogen peroxide, producing water. For example, look at the L-ascorbate peroxidase, which catalyzes

  L-ascorbate + H2O2 → dehydroascorbate + 2 H2O

Beside these reaction, there is also a lot of water which doesn't react and is simply excreted after having served its purpose. So, while some water is "converted", some other part "passes through".

The reactions are balanced in such a way that normally, you excrete the same amount of water as you drink, as explained in Amory's answer. But despite this balance of the amount, you cannot claim that the water just passes the body unchanged. Some molecules of it are used up, and others are created de novo.


Can human brain memory be removed by EMP? The human brain is the most complicated human organ so it is hard to examine it completely but based on what we know do you think (or do you know from some source) if a human memory can be removed by emp(electromagnetic pulse) ? (If so do you think it would be pernament or temporary?)

http://en.wikipedia.org/wiki/Electromagnetic_pulse mentions the following natural sources of EMP, which I have ordered by frequency / period, from the shortest to the longest:

Electrostatic discharge from objects coming into contact (normally too small to be of any concern)
Lightning (milliseconds)
Solar flares (hours.) Such flares cause geomagnetic storms (more on this later.)

Several artificial sources of EMP are mentioned, of which the only ones of interest are military:

Non-nuclear weapons. The page links to a general article on directed-energy weapons, which mentions microwave devices for causing pain and for targeted damaging of electronic equipment.
Nuclear weapons. http://fas.org/nuke/intro/nuke/emp.htm gives more information on this, listing three phases.

  The EMP produced by the Compton electrons typically lasts for about 1 microsecond, and this signal is called HEMP. In addition to the prompt EMP, scattered gammas and inelastic gammas produced by weapon neutrons produce an “intermediate time” signal from about 1 microsecond to 1 second. The energetic debris entering the ionosphere produces ionization and heating of the E-region. In turn, this causes the geomagnetic field to “heave,” producing a “late-time” magnetohydrodynamic (MHD) EMP generally called a heave signal.

The same reference also indicates:

  ...the region where the greatest damage can be produced is from about 3 to 8 km from ground zero. In this same region structures housing electrical equipment are also likely to be severely damaged by blast and shock.

As far as I am aware, memory loss was not a major recorded symptom among the survivors of Hiroshima and Nagasaki. The only recent data for sufferers of EMP would be from victims of lightning stikes. While the frequency spectrum is admittedly different from nuclear weapons, victims of lightning strikes are surely subjected to greater magnitudes of EMP than those who managed to survive nuclear bombings (who suffered many other traumas, such as blast waves and radiation.) Those who survive the immediate physical (burns) and neurological (cardiac arrest) effects of lightning strikes must surely be knocked unconscious and be disorientated when they regain consciousness. But again, I am not aware of medium or long term memory loss being a particular symptom.

It is worth comparing the structure of the brain (a fairly homogenous mass of tissue of high water content, relatively conductive) with the structure of electronic equipment (components of ever smaller size and greater resistance in order to save power, surrounded by a nonconductive medium such as air, and interconnected by wires, which serve to channel voltage.) It is unsurprising that the brain is less subsceptible to electrostatic damage than electronic components (electronics workers have to take precautions in order to avoid damaging sensitive components with static discharges from their bodies and clothing.)

The most widespread damage to equipment caused by EMP is from the long-period pulses, which are channeled by electric cables. These act over distances much larger than the size of the human body.

From the last reference:

  ...distortion of the geomagnetic field was observed worldwide in the case of the STARFISH test. ... the signal from this process is not large, but systems connected to long lines (e.g., power lines, telephone wires, and tracking wire antennas) are at risk

and

  The first recorded EMP incident ... nuclear test over the South Pacific ... resulted in power system failures as far away as Hawaii.

http://en.wikipedia.org/wiki/Geomagnetic_storm mentions cases of damage caused by long period EMP, including electric shocks suffered by telegraph operators during solar flare events.

So in conclusion, any amnesia caused by EMP is likely to be caused by normal biological shock mechanisms to individuals unfortunate enough to be electrocuted, and not by any direct electrical effect on the brain itself.


Why do recessive lethal genetic diseases continue to exist? I'm trying to understand, in a simplistic representation of a recessive genetic disease (e.g. Tay Sachs), why wouldn't it "disappear" over time (many generations). Please excuse the use of non-professional terminology below, I hope the point I'm trying to make will be clear.

Let's assume that, for simplicity, people marry at random and each couple has 4 children. Denote the probability of carrying the "bad" gene by p, then a couple of 2 non-carrying people will have 4 healthy children, a mixed couple will have, on average, 2 healthy and 2 carrying children, and a couple of 2 carrying people will have 1 healthy, 2 carrying, and one sick child (which we assume will not have children so we ignore it in further calculations).

Assuming large enough population and random couples and everyone gets married (for simplicity):
The probability of a couple of non-carrying: (1-p)^2
The probability of a mixed couple: 2 * p * (1-p)
The probability of a 2-carrying couple: p^2

The expected number of healthy children per couple: 4*(1-p)^2 + 2*2*p*(1-p) + p^2 = 4 - 8*p + 4*p^2 + 4*p - 4*p^2 + p^2= 4 - 4*p - p^2 = (2-p)^2
The expected number of carrying: 2*p*(1-p) + 2*p^2 = 2*p - 2*p^2 + 2*p^2 = 2p

Dividing to get the new probability for carrying the gene:
2p / (2-p)^2
Which for small enough p is clearly smaller than p (e.g. for p = 0.05 we get ~0.0263).

If I'm not mistaken this means that the number of those carrying the genes should become exponentially small (in the number of generations).

I realize this is a very simplistic model, marriages are not random, mutations occur etc. but I would expect the basic intuition to hold. What am I missing?

Firstly, sorry if this is not so much an answer as a comment, but it is too long to put in the comments section, although I'll try keep it concise...

I can see exactly what you're doing however my math differs at points, and would appreciate you looking over it.

"The expected number of healthy children per couple: 4*(1-p)^2 + 2*2*p*(1-p) + p^2 = 4 - 8*p + 4*p^2 + 4*p - 4*p^2 + p^2= 4 - 4*p - p^2 = (2-p)^2"

Is it not: ... =  4 - 8p + 4p^2 + 4p - 4p^2 + p^2 = 4 - 4p + p^2 = (p-2)^2

Furthermore: "The expected number of carrying: 2*p*(1-p) + 2*p^2 = 2*p - 2*p^2 + 2*p^2 = 2p" - why for the probability of carriers in mixed couples - "2*p*(1-p)" - why have you not multiplied through by two (as with expected healthy children), given that as you said "a mixed couple will have, on average, 2 healthy and 2 carrying children"?

Is it not: 2 *2p(1-p) + 2p^2 = 4p - 4p^2  + 2p^2 = 4p - 2p^2 = 2p(-p + 2)

In this respect I got different expectations. Lastly "Dividing to get the new probability for carrying the gene..." You have done (no. healthy) / (no. carriers). Is the probability for carrying the gene not (no. carriers)/(no. carriers + no. health) - that is the no. carriers as a fraction of the entire population to give a probability?

Using my expectations this would be: [2p(-p+2)] / [2p(-p+2) + (p-2)^2] = [2p(-p+2)] / [-2p^2 + 4p + p^2 - 4p +4] = [2p(-p+2)] / [-p^2 + 4] = [2p(-p+2)] / [(-p + 2)(p + 2)] = 2p / (p+2)

Therefore, with a new probability for carrying of 2p / (p+2), for our "hypothesis" of the diminishing probability of carrying to stand, we need the condition 2p / (p+2) < p to stand, solving for p:

2p < p(p+2) -> 2p < p^2 + 2p -> 0 < p^2 -> p > 0

Since, as a probability, p must be <= 1, and assuming (as we are) that carriers exist and so it must be > 0, p always satisfies this condition - ergo I would conclude that for any value of p - not just small, the probability of carrying will diminish in the next generation. Just as we "hypothesised". However a quick google of "plot y = 2x/(x+2)" would indicate to me that as p approaches 0 it's rate of "diminishing" actually decreases, and it does not get exponentially smaller as you indicated. But solving for y = 0 gives x = 0 so this model would suggest the gene is never actually fully eradicated?! Which of course confuses me, although on a macro scale it might make sense, as you can't have, for example, 0.1 children "carrying", and 99.9 "healthy", only 1 and 99 or 0 and 100.

Thanks for reading this far, any response would be really appreciated, especially given I might be miles off.

Philip.


Why are mice with a single X chromosome and no Y chromosome males? I was searching online and I read this article Mice can be male without Y chromosome and this is a part of it:

  The experiments demonstrate that there are multiple ways to make males, says Richard Behringer, a developmental geneticist at MD Anderson Cancer Center in Houston. “They’ve done it without any Y chromosome gene information,” he says. “There’s not even a sniff of the Y around.”

I know that mouses are separated to males and females, and they both necessary for reproduction. Can someone please explain to me how could this possibly be? there's a lot of biology specific terms that i did not understand well

Almost all mammals (including mice and humans) have two sexes where the males have a Y chromosome and an X chromosome (whereas females have two X and no Y chromosomes).  This is not the only way organisms can determine sexes, but it's the way mammals evolved to do it.

So how does having a Y cause an individual to be male?  The Y has only a few genes (less than all other chromosomes), but it has genes that occur only on the Y.  One of these in particular, the one called SRY, is the main gene that causes the individual to develop male characteristics.  It mostly does its job indirectly, by making a protein that affects many other genes on other chromosomes that in turn do the work of building and maintaining the male form.

In the experiments reported by the article mentioned in the question, they managed to cause mice without a Y chromosome to develop many male characteristics.  They did this by faking one or two of the actions of SRY.  One of the many actions of SRY is to turn on a gene called Sox9 (which is on a non-Y chromosome), and it turns out Sox9 causes most of the things that make the male mouse form.

So the experimenters found a way to turn on Sox9 without using SRY or anything else from a Y chromosome.  This got them mice that looked male, but didn't produce sperm.  So they did something further that substituted for a Y chromosome, and caused a weak gene on the X to work at many-times strength to do the job that a strong Y gene normally does.  This caused the special "male" mice to produce sperm.  But these sperm were not fully functional (they couldn't swim and enter the egg), so they showed they were essentially sperm by simply using a tiny needle to inject the semi-functional sperm into mouse eggs and have those eggs develop into viable baby mice.

Bottom line, if you use artificial methods to do what the Y chromosome does, you can make male mice which do not have a Y chromosome (and learn some things in the process).


Besides fruits and milk, what other things in nature are "intended" to be eaten? Besides fruits and milk, what other examples are there in nature where it is beneficial for a species to have some part of its biomass eaten by others so that it evolved to produce nutritious parts to be eaten by other organisms? For example, plants having animals eat their fruits as a means of transporting their seeds.

Update.

I think there are at least two philosophically different scenarios that interest me.

One is when the substance is intended to be eaten by the same species (example: milk).

The other is when it is intended to be eaten by another species (example: fruits).

There are plenty of examples! Here is a short list

Defence ("Eat that so that you don't eat this")

Evisceration. It is the ejection of internal organs so that predator eat them but not the prey entirely. (sea cucumber does evisceration)
Lizard's tail being fragile on purpose

Parental care

Milk
Regurgitation
Sexual Cannibalism (as it is often hypothesized as benefiting the male also as he indirectly nourish his offspring)
In haplo-diplontic species, one of the two generation can be much bigger and can transfer its nutrient to the other generation (offspring), such as in moss for example.

Mutualism

Nectar
Fruits
Honeydew produced by aphids to attract ants which protect them from predators
Ant breeding fungi

Symbiosis

Lichen
Root nodule

Social behaviour

Honeypot ant (if we are happy to consider the honey stored in the ant for a long being part of the ant biomass).

Human related

The researcher in parasitology that feed his mosquitoes with his own blood!
Crops (and other things) under artificial selection. It is here just cases of mutualism where humans is involved.


What is meant by "50% related to sibling" versus "95% related to chimpanzee"? Obviously I am more related to my sister than to a chimpanzee, so what do these different percentages actually refer to?

Here is my preliminary research:

https://genetics.thetech.org/ask-a-geneticist/siblings-are-around-fifty-percent-related/

https://genetics.thetech.org/ask/ask395/

50% related to sibling means that, out of the portion of the genome that vary in humans, you share half of them with your sibling. (if you compared total genetic match not just ones that actually vary in humans you are looking at something closer to  ~99.95% match)  Now because because variations are not evenly distributed and your parents likely came from the same source population you usually share more with a sibling, but recombinations has a random aspect, and sex chromosomes have a large effect as well. So 50% would be the average using the most common methods of comparison, and even then it is only shorthand. It is a calculation more than a conclusion, if you are 50% related to your parents and so is your sibling then the probability calculation is [0.5 X 0.5 = 0.25]  Note this is in humans, other animals use different chromosome distributions which can result in different numbers, bees for instance have haploid males making females siblings far more closely related.

95% identical to chimpanzee means out of all the genetic elements only 5% of human ones are unique to humans (or chimps) and not shared by chimps and humans while 95% is shared by both. 95% is a lower estimate because they are using the strictest comparison.

One important thing to consider is there are many ways to compare genetic variance, consider a book as an example, if I switch 2 chapters is that one change, two changes, or hundreds of changes (by the number of letters or words in the chapters). because criteria are different you get slightly different estimates of difference. In the case of the 95% estimate that would be using the "hundreds of differences" method of comparing. Deleting the sentence "Mary had a little lamb" would be 21 changes using this method. Other methods would consider it only one difference since it is the product of a single mutation.


Why is the central tendon of diaphragm called a tendon? Why is the central tendon of diaphragm called a tendon when it does not connect the diaphragm to any bone?

A tendon usually connects a muscle to a bone, but not always.

According to InnerBody, the diaphragm muscle originates at the lumbar vertebra, lower ribs and sternum and inserts to the central tendon.

  The central tendon — a flat aponeurosis made of dense collagen fibers
  — acts as the tough insertion point of the muscles.

So, the central tendon acts as the diaphragm's own insertion.

A similar example is aponeurosis of the external oblique muscle in the lower part of the abdominal wall (Brazosport.edu, Picture 10.11.a.).

A tendon is the connective tissue that is always a part of a muscle and it fixes the muscle during its contraction.

A ligament is the connective tissue that merely connects two bones or two internal organs and is not actively involved in their movements.


How does the embryo inside a shelled egg get oxygen? If I'm not mistaken a typical animal in the womb will get oxygen via the umbilical cord from the mother. Thus allowing it to "breathe" in a liquid environment. I thought maybe shells are permeable and allow air to come in through the shell, but then I thought of eggs laid in the ground like turtles do.

How do animals in soft/hard shells get their oxygen?

The key point in both cases is that the eggshell and membrane are permeable to oxygen, as you thought. There are subtleties - for instance, the oxygen-permeability of avian (hard-shelled) eggshells changes during development.

In the case of eggs laid underground, as in sea turtle eggs, the leathery shell is still permeable to oxygen. The sand restricts oxygen flow, but turtles seem to take care to not bury their eggs too deep for oxygen to diffuse to their developing nest.


Fate of erythrocytes after splenectomy The spleen is considered a graveyard for red blood cells. So in case of Splenectomy (complete surgical removal of the spleen), what would be the fate of red blood cells? Would this cause Polycythemia?

The spleen is not the only organ which removes "old" erythrocytes, this happens as well in the liver and the lymph nodes. The whole process is termed Eryptosis, the Apoptosis of Erythrocytes. During the aging of erythrocytes sialic acid on their outer membrane surface is removed. This leads to the recognition by macrophages and phagocytosis of this cells by macrophages which are located in liver and spleen. For more information see this article: "Physiology and Pathophysiology of Eryptosis"

Polycythemia is the state when you have an elevated number of red blood cells, characterized by an increased Hematokrit level. This is caused by the over-production of red blood cells, which can be caused by an overproduction of hematopietic cells in the bone marrow (so called myeloproliferative syndrome, which are basically cancers), the exposure to permanently low oxygen-levels (this is what athletes exploit when the do training at high altitudes) or malignancies (usually lymphoma). It is also possible due to the mis-use of Erythropoietin (EPO) which induces the production of red blood cells. Another possibility for having too much red blood cells is the over-transfusion during a blood transfusion. For further information have a look into the Wikipedia. The article there is pretty complete and contains a number of references.


what's the difference between traditional genetic engineering and and CRISPR? While at school, I learnt about restriction enzymes and how you could insert foreign DNA into an organism.

When I first heard about CRISPR I thought it was very similar except much more precise/targeted.

It seems however that CRISPR only allows editing (substituting nucleotides)

What are the differences, advantages, etc?

Bacteria and archaea evolved CRISPR as part of their adaptive immune system to protect themselves from invading viruses and foreign plasmids. The defence system relies on small, non-coding RNA molecules (CRISPR RNAs/guide RNA) that in association with a CRISPR associated (Cas) protein silence foreign sequences by means of cleavage. Twenty nucleotides at the 5’ end of the CRISPR RNA, corresponding to the protospacer region, direct the Cas9 protein to a specific sequence within the DNA using predictable Watson and Crick base pairing between the target DNA and the guide RNA, triggering enzymatic cleavage of the foreign DNA. Essential for cleavage is the presence of a sequence motif immediately downstream of the target region, known as the protospacer-adjacent motif (PAM),the PAM sequence in S. pyogenes (the most widely used system) is NGG. Because a sequence match also exists between the guide RNA and the host’s DNA that encodes it, it is vital that the guide RNA identifies bona fide targets without attacking the host chromosome. Discrimination between the target and host protospacer is achieved by the Cas effector recognition of a PAM sequence that initiates binding and cleavage of the foreign DNA. Changing the DNA target site that is specified by the 20 nucleotides at the 5’ end of the guide RNA redirects the system to target a different DNA sequence, making it a highly versatile and programmable tool. In 2012, the CRISPR system was  programmed to cleave specific DNA sites in vitro and since then, the system has been widely used in many gene modification applications.

CRISPR allow so much more than just substituting nucletodies. Like you say, CRISPR is a much more precise system than restriction enzymes, the guide RNA for CRISPR systems is typically around 20 nucleotides long so it can theoretically be used to target a unique site in the genome (4^20 = 10^12, so only the recognition site is expected to feature once 1 in 10^12 bases, N.B. the human genome is only 3x10^9 base pairs in size).

There are several options using the CRISPR with an active Cas9 protein, the first is to create a gene knockout, which removes the function of a gene. Gene knockouts can be performed by targeting the CRISPR-Cas9 system to the start of the gene and cleaving both strands of the DNA to generate a double stranded break which will be repaired most likely by the cellular repair pathway non homologous end joining (NHEJ). NHEJ results in insertions or deletions and so will most likely result in a frameshift mutation which alters a large amount of the amino acid sequence in the gene or introduces an early stop codon, so the protein produced is non functional. Alternatively a conserved residue (e.g. a catalytically important residue) in the protein can be targeted and mutation of this can remove the catalytic function or recognition domain in an enzyme or protein. NHEJ can also be used to mutate DNA that codes for RNA products. Additionally, the CRISPR system can be targeted to regions outside of the coding sequence such as the promoter or enhancers and silencers/operators (depending on whether prokaryotic or eukaryotic), which can also remove the functionality of the gene.

The CRISPR system can also be introduced to the cell  together with a single-stranded or double-stranded DNA template to make very small and precise changes to the DNA (e.g. single base mutations), or insert DNA sequences up to thousands of bases in length so that entire genes can be incorporated into the target region. This more precise editing method also involves the double stranded break formation by the cas9 protein, but relies on different cellular repair pathways: homology directed repair, the most common form of which is homologous recombination. Importantly, the template DNA must have homologous sequences to the DNA flanking either side of the double stranded break. In the presence of the correct exogenous DNA template, homology directed repair can occur in which the exogenous template DNA is incorporated into the target DNA in exchange for the damaged DNA.

Other use of CRIPSR include using a catalytically inactive cas9 protein (dead Cas9). This system is unable to cleave DNA, but is still able to target specific sites in the DNA. dead Cas9 can be fused to or recruit effector proteins for regulating gene expression at the transcriptional level, as well as guiding enzymes capable of precise base editing without introducing double stranded breaks. The dead cas9 system can be fused to transcription repressor domains such as the Krüppel-associated box (KRAB) or transcriptional acitvators such as VP64 for effective and specific repression or activation of gene expression at sites that don't contain recongion sequences for these effectors. dead Cas9 can also be used to recruit epigenetic modifitying enzymes such as methylases and acetylases to regulate gene expression this way. Additionally, this system can be fused to DNA base editors, which are enzymes created by directed evolution that are capable of causing efficient and specific point mutations in DNA and RNA (this is much more specific and effective than point mutations using homology directed repair), although RNA editing required using cas13.

Gene editing can be used to repair disease causing mutations, introduce new genes with novel functions into organisms' genomes, transiently alter gene expression to treat diseases; create knockout, knockdown and knock in strains for studying the effects of genetic factors on phenotype and even more.

In contrast, restriction enzymes typically have recognition site of 6 nucleotides and so they will cut at many orders of magnitude more sites than CRISPR will (4^6 = 4096, so 1 in 4096 nucleotides are expected to be a cut site for restriction enzymes) so they are not suitable for specific editing of genomes as they will cause non specific fragmentation of genomic DNA, which will kill the organism, so CRISPR is a much better enzyme for editing genomes. Instead, restriction enzymes are used in molecular cloning to generate sticky overhangs (or blunt ends) for the assembly of DNA molecules to generate recombinant DNA.

Although the PAM appears to limit the number of target sites that the CRISPR system can be targeted to (around 1 in every 16), through directed evolution, a Cas9 variant with increased PAM compatibility has been developed. This new Cas9 is capable of recognizing PAM sequences including NG, GAA, and GAT, this makes it  more versatile and greatly expands the number of targets available for site-sensitive genome editing applications.

Whilst CRISPR based gene editing is very exciting, a lot of work is still needed to: increase the specificity of the system as it causes numerous off site mutations, which can be lethal to cells; to increase the effectiveness of delivery of the system in vivo to large organisms such as humans; to reduce the immunogenicity of the system (it can trigger an immune response in humans) so that it is safe to use; as well as increase our understanding of the affect of making specific mutations in humans (e.g. which mutations can treat diseases safely).

References/further reading:

Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science (80-. ). 337, 816–821 (2012).

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression. Cell 152, 1173–1183 (2013).

Liu, X. S. et al. Editing DNA Methylation in the Mammalian Genome. Cell 167, 233–247.e17 (2016).

Zalatan, J. G. et al. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160, 339–50 (2015).

Hu, J. H. et al. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature (2018). doi:10.1038/nature26155

Cox, D. B. T. et al. RNA editing with CRISPR-Cas13. Science (80-. ). 358, 1019–1027 (2017).


Are there animal models for Clostridium difficile that better replicate human infection than hamsters? So I'm looking for some information on the infectious dose necessary to colonize a human with Clostridium difficile. There's no human challenge studies, and since it's not a foodborne pathogen, little we can get from outbreak data.

Which leaves me looking at animal models, to at least get the shape of the probability of infection based on a given dose. But the papers on hamsters makes it appear that they're infected rather easily, and that this infection is particularly severe.

Is there another animal model that more closely mimics the infection dynamics of C. difficile in humans?

Hamsters are considered the best animal model, most studied.
C. difficile has been found in calves, ostriches, chickens, elephants, dogs, horses, and pigs, but its role in infection and its pathogenesis in animals are largely poorly understood and possibly underestimated


How is a stem-cell induced to assimilate a knock-in DNA construct? While looking at (daylight) color perception I came across a paper by Jeremy Nathans (et al., Proc. Nat. Acad. Sci., vol. 100 no. 20, 2003, full text here) in which he describes the creation of a mouse with genetically modified vision.

My threshold question is just about the mechanics of the process, which he characterizes as "site-directed mutagenesis." My understanding (a guess, really) is that embryonic stem cells are induced to assimilate homologous human DNA sequences and these cells are injected into mouse blastocysts.

In outline I understand the idea of the DNA construct but wonder physically how the stem cell initially acquires the knock-in construct.

Thanks for any enlightenment.

Edit: I see that there are several ways to do this and that the paper's "Materials and Methods" section focuses on the molecular genetic details. Maybe we can't get the information from the four corners of the document? If so I'd still be interested in whatever process seems likely given the sort of mouse they made. Thanks.

There are two ways to introduce genetic material past a cell membrane. Infection and generation of a porous cytoplasm. Viruses and bacteria generally are used. Retroviruses tend to cause leukemia so they are avoided however they are the only way to get past the nucleus in vivo of multicellular life. Electroporation and needles generate a porous cytoplasm allowing genetic material to seap or be inserted into the cell.

Once the genetic material is in the cell it has to have contained site specific oligonucleotides to hybridize with the strand of interest.

  Procedure

  The procedure for making mixed-genotype blastocyst.

  Breeding scheme for producing knockout mice. Blastocysts containing cells, that are both wildtype and knockout cells, are injected into the uterus of a foster mother. This produces offspring that are either wildtype and coloured the same colour as the blastocyst donor (grey) or chimera (mixed) and partially knocked out. The chimera mice are crossed with a normal wildtype mouse (grey). This produces offspring that are either white and heterozygous for the knocked out gene or grey and wildtype. White heterozygous mice can subsequently be crossed to produce mice that are homozygous for the knocked out gene.
  There are several variations to the procedure of producing knockout mice; the following is a typical example.

  The gene to be knocked out is isolated from a mouse gene library. Then a new DNA sequence is engineered which is very similar to the original gene and its immediate neighbour sequence, except that it is changed sufficiently to make the gene inoperable. Usually, the new sequence is also given a marker gene, a gene that normal mice don't have and that confers resistance to a certain toxic agent or that produces an observable change (e.g. colour or fluorescence).

  Stem cells are isolated from a mouse blastocyst (a very young embryo) and grown in vitro. For this example, we will take stem cells from a white mouse.
  The new sequence from step 1 is introduced into the stem cells from step 2 by electroporation. By the natural process of homologous recombination some of the electroporated stem cells will incorporate the new sequence with the knocked-out gene into their chromosomes in place of the original gene. The chances of a successful recombination event are relatively low, so the majority of altered cells will have the new sequence in only one of the two relevant chromosomes - they are said to be heterozygous.
  The stem cells that incorporated the knocked-out gene are isolated from the unaltered cells using the marker gene from step 1. For example, the unaltered cells can be killed using a toxic agent to which the altered cells are resistant.

  The knocked-out stem cells from step 4 are inserted into a mouse blastocyst. For this example, we use blastocysts from a grey mouse. The blastocysts now contain two types of stem cells: the original ones (from the grey mouse), and the knocked-out cells (from the white mouse). These blastocysts are then implanted into the uterus of female mice, where they develop. The newborn mice will therefore be chimeras: some parts of their bodies result from the original stem cells, other parts from the knocked-out stem cells. Their fur will show patches of white and grey, with white patches derived from the knocked-out stem cells and grey patches from the recipient blastocyst.

  Some of the newborn chimera mice will have gonads derived from knocked-out stem cells, and will therefore produce eggs or sperm containing the knocked-out gene. When these chimera mice are crossbred with others of the wild type, some of their offspring will have one copy of the knocked-out gene in all their cells. These mice will be entirely white and are not chimeras, however they are still heterozygous.

  When these heterozygous offspring are interbred, some of their offspring will inherit the knocked-out gene from both parents; they carry no functional copy of the original unaltered gene (i.e. they are homozygous for that allele).
  A detailed explanation of how knockout (KO) mice are created is located at the website of the Nobel Prize in Physiology or Medicine 2007.

-wikipedia


Are these 3.5B year old fossils the oldest on earth? The following commentator writes:

  Researchers at UCLA and the University of Wisconsin–Madison have confirmed that microscopic fossils discovered in a nearly 3.5 billion-year-old piece of rock in Western Australia are the oldest fossils ever found and indeed the earliest direct evidence of life on Earth.

It seems strange that this would come up recently. I thought there might be something older.

My question is: Are these 3.5B year old fossils the oldest on earth?

Yes, the study was peer reviewed and published less than a month ago (Dec 18, 2017) in PNAS, among the most prestigious journals in science by qualified experts. They could be wrong of course, like all science. But there is no reason I can see to doubt their work.


Tool for translating chomosome, index numbers to sequence information Is there a tool which allows me to transform information in the form (chromosome number, start index, end index) to sequence information? For example, something like (6, 43770819, 43770841) should yield GACCCCCTCCACCCCGCCTCCGG as this is the relevant bases on the 6th chromosome.

A command line executable is preferred, although a web-based service is also fine. Thanks a bunch in advance.

You can write a small script to do that. Basically you just have to print a string from position-x to position-y. Explaining how to do that is not really on-topic here.

From available tools you can use getfasta from the bedtools package. This requires a BED file, or a GTF file  as an input. The three column format as in your question will also work but usually the orientation (+/-) is also important to fetch the right sequence; otherwise all sequences would be fetched from the + strand only. GTF format is a bit different: the three columns in your question would be the first fourth and fifth column in the GTF. Seventh column holds the orientation.

bedtools getfasta [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF> -fo <output FASTA>

(or):

getFastaFromBed [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF> -fo <output FASTA>

There is another one called gffread which comes with the tophat package.

gffread takes a GTF/GFF file as an input and gives you a fasta file of sequences corresponding to the positions listed in the GTF file. The third column (feature) should be exon or transcript as this tool was actually designed to extract transcript sequences.

gffread -w transcripts.fa -g /path/to/genome.fa transcripts.gtf


Where can I find a full genealogy of human cell types? It is said on Wikipedia, that the precursor of blastocyst is a morula, and that the precursor of morula is a zygote. This gives us the part of genealogy tree of cell types. Unfortunately, no full genealogy can be found in Wikipedia.

Where can I find a more complete picture, preferably a full tree of cell types including information about each type?

Wikipedia has a page listing cell types which classifies their origin as endodermal or ectodermal.

I haven't been able to find a source for a complete lineage of all cell types, and I have gained the impression that there is no complete picture, except in some specific cases such as the haemopoietic lineage.

Here is a TEDX talk by a researcher in the field, and here is a slideshow by the same person which lays out the problem and its importance.


How to set the phenotype in GWAS analysis? In the GWAS analysis, my animal sample phenotype is whether an individual dies or survives. And I have every sample death time. How do I set the phenotype in GWAS analysis?

Simply, First of all, you can group samples as survived animals and dead samples and you have a binary phenotype.

In a different approach, you can use survival time (time to death) as an ordinal variable phenotype. If you want you can utilize survived sample by assign a large death time value to them.

In the third approach, you can cluster the survival time (time to death) into the desired $n$ groups by the simple procedure like $k$-means. and you have coarse grain ordinal variable you can add survived sample group at the end of The Spectrum.


Quick overview of how to capture microscope images of histology plate or fluorescent plate I am looking at these two:

I would like to DIY take photographs of plant and animal cells using a cheap microscope such as this:

I don't know too much about microscopes or the techniques to do the staining, but that is what this question is about. I would like to know briefly what is required (tool-wise and material-wise) to capture images like the two above.

For fluorescent microscopy images, wondering if I actually need a fluorescent microscope, or if I can make do with a regular optical microscope. If I need a fluorescent one, wondering if there is anything else needed, like special lighting or special materials for tagging the cells, which seems like it might require extra stuff like centrifuge and who knows what else. In that case I would just like to get a sense for how complicated it is to do fluorescent microscopy.

For the histology slides, wondering generally what it takes to do that too, if I can get by with a regular microscope.

Generally wondering what equipment is required to accomplish these two images.

So far I have a DSLR camera and am imagining a basic optimal microscope with a DSLR adapter, and perhaps some basic dies that I would just drip into the slide (don't even need a pipette). That just shows my simplistic understanding, maybe fluorescent microscopy requires advanced biotechnology of some sort, which is sort of what I'm wondering, what the basics are.

For fluorescent microscopy images, wondering if I actually need a fluorescent microscope, or if I can make do with a regular optical microscope.

You need a fluorescence microscope. You need to be able to excite your sample with a narrow wavelength of light, and then image a different wavelength of light that is emitted. You need mirrors, emission and excitation light filters for that. You also need to understand the process. If you don't, having software to do the 'thinking for you' such as overlaying the different color channels is a nice thing, but then it's another requirement.

  If I need a fluorescent one, wondering if there is anything else needed, like special lighting or special materials for tagging the cells, which seems like it might require extra stuff like centrifuge and who knows what else.

Samples can sometimes have autofluorescence (e.g. the chitin that makes up the cuticle of insects is autofluorescent) but most samples are not. Almost always a fluorophore is used to stain the specimen for something. These can be cheap or very expensive, depending on what you want to stain. This really depends on your sample and how it is prepared. And know that most 'good' samples' are dehydrated or are treated by chemical fixation, which requires chemicals you cannot usually find at a local pharmacy. It depends on how ambitious you want to get as an amateur microscopist!

Also, you won't need a centrifuge.

  For the histology slides, wondering generally what it takes to do that too, if I can get by with a regular microscope.

You can get by with a regular upright widefield microscope for sure. If you perform the sectioning well (making thin slices of your sample) then even basic microscopes will produce fascinating images, provided your lighting is good. It helps to have a condenser or a nice lamp and some thin and clean glass slides for well illuminated images.

  Maybe fluorescent microscopy requires advanced biotechnology of some
  sort, which is sort of what I'm wondering, what the basics are.

It requires a little bit more optical work. I would stay away from it unless you are serious, because it takes quite a bit more work and equipment to make it minimally workable. Normal microscopy is certainly a lifetime of fun if you have the desire to find interesting samples and work to make them good for imaging.

Addendum: the principle of fluorescence microscopy is quite simple but aligning everything is actually quite difficult if you are an amateur with no specialized tools. Here is the principle only, notice how the input and output must be aligned and the small objective lens has to transmit both excitation and reflected light:

And here is an example of a basic lab stain for two elements of the cytoskeleton (actin in red and microtubules in green) and a DAPI-type stain for nucleic acids (that shows you the DNA-rich nucleus in blue). The crispness of the image really depends on the use of at least two or three lasers (not epifluorescent illumination, i.e. "lamp nearby") to produce the necessary and specific narrow excitation to separately image the different channels. The light detectors are in black and white (for increased resolution), and only in post-processing are they color-coded to make the image pretty.

For a start I would begin with the basics! Pollen, cells on the inside of your cheek, blood, a single onion layer (...is a monolayer of cells, perfect for imaging), anything else you find and can think of! And find yourself a nice stain, or a nice dye or ink that is partially permeable. The world is your proverbial oyster at this point.


What is the difference between a fixed substitution and a single nucleotide polymorphism (SNP)? I recently read a report that stated "We found 430 fixed substitutions […], with an additional 34 single nucleotide polymorphisms (SNPs) fixed within individual patients." What is the difference between both terms?

If you look into a certain population, you will find mutations (for example SNPs) in some ratio with the wild-type allele. When a mutation reaches fixation, it will be the only allele, reaching 100% penetrance in this population. See here for more information.

In the context given I would interpret it in the way that a total of 464 SNPs were found, 430 of these were in fixation (so can only be discovered when comparing them to another population) and 34 SNPs which haven't reached fixation and thus cannot be found in all members of the population.


Why does organ transplant work although it seems organ's motor neuron isn't connected to recipient's CNS Although it seems impossible with current technology to connect organ's capillaries to the recipient's capillaries and its motor neuron to the CNS, transplanted organ works for years. But why?

Capillaries only transport blood for short distances, and within an organ. The blood supply to/from a major organ is generally carried over a few major blood vessels (usually one artery, one vein). Splicing such larger blood vessels are what surgeons earn their pay to do.

In terms of nerves, most transplanted organs function fairly well without being connected to the CNS.


Can a protein kinase phosphorylate both a threonine and tyrosine residue? I know that some kinases can phosporylate both serine and threonine residues because of their structural similarities, but can such a kinase phosphorylate a tyrosine residue as well?

If not, then why?

Ony a few protein kinases can phosphorylate all three amino acids — these are classified as dual-specific kinases (EC 2.7.12.1). Examples are APK1 from Arabidopsis or MEK kinases in mammals.

As with other enzymes, the residues at the substrate binding site determine which substrates can be accomodated there. Structures or Ser- Thr- and Tyr-kinases are available for inspection, should you wish to explore them.


TB disease - treatment and infection Background: I'm currently performing research in mathematical biology,
specifically on the treatment dynamics of HIV and TB co-infection.

Question: Can a person infected with TB disease, who are undergoing treatment for it, infect a person with no history of TB bacteria in their body?

Reformulation: In other words, is there a similar analogue for TB as for HIV, wherein an HIV+ person undergoing treatment for HIV will have a lowered viral load and thus have negligible chances of infecting a person with no history of HIV?

Please note that my model does not incorporate latent TB because it would become too complicated to analyze. I am focusing only on TB disease because only it is infectious.

Thanks for any help.

First there is one major difference between HIV and TB: As long as the TB bacteria are still susceptible to treatment (which is developing into a major problem in some regions of the world) there is a effective treatment which can eradicate the infection. For HIV this is not possible. Here we can only lower the viral load (sometimes under the detection limit), but when the treatment is stopped, the virus will return.

Then it seems that patients under treatment of a drug susceptible TB are infectious for a longer time than previously thought. Until now they have been isolated at the beginning of the treatment (typically around the first two weeks) until three consecutive sputum samples had been negative. Then they were released from isolation and thought to be non-infectious. At this point they are not cured, the treatment has to go on for several weeks.

Now there is newer research indicating that patients can still be infectious although they are under treatment and have negative sputum samples. It seems here that the currently used detection method is not sensitive enough. See these references for more information:

How Many Sputum Culture Results Do We Need To Monitor
Multidrug-Resistant-Tuberculosis (MDR-TB) Patients during Treatment?
High incidence of tuberculosis, low sensitivity of current diagnostic
scheme and prolonged culture positivity in four colombian prisons. A
cohort study.
Prolonged infectiousness of tuberculosis patients in a directly
observed therapy short-course program with standardized therapy.


Breeding laboratory mice with cancer; how does this work? It has recently been brought to my attention that live laboratory mice with specific cancer strains can be readily purchased for medical research.  For example, the Jackson Laboratory sells mice with a wide range of strains of cancer (with price depending heavily on the type of cancer desired).

  Question: What is the general process behind breeding laboratory mice with specific cancers for medical research?

Cancer is a highly genetic disease, and much is known about how different genetic mutations contribute to the generation, growth, proliferation, metastasis, and control of tumors. Jackson Labs (commonly known as Jax in the research community) provides literally thousands of strains of mice, each bred/genetically engineered to have certain genotypes and/or phenotypes, a good proportion of which can be used for various purposes in cancer research.

I'll take a very basic example to walk you through the creation of a "cancer mouse." Say I've been doing research and have found through studying the DNA of many patients that the ABC123 gene seems to be associated with a certain type of cancer (skin, for example). I want to know more how ABC123 works, so one of the first things to do is to find out what (if anything) goes wrong when it isn't there - when it gets "knocked out." Using genetic engineering techniques, I create a sequence of DNA (called a vector) that matches the "wild-type" (WT) or normal mouse ABC123 gene sequence at the ends, but in the middle has a certain selection gene called Neo instead of the rest of the ABC123 sequence:

Neo makes cells that it is in resistant to a certain antibiotic called Neomycin or Geneticin, also called G418. I take my targeting vector and electroporate it into mouse embryonic stem cells (ESCs) that, if implanted into an appropriately-prepared female mouse, could develop into a normal mouse embryo. I then culture these ESCs in the presence of neomycin, which will kill any cells that haven't taken up and incorporated the vector into the genome.

Once I have some cells that I know have taken up the Neo part and are missing the targeted part of the gene (the exons marked 1, 2, and 3), I inject a few cells each into mouse blastocysts, where they divide and differentiate to form various parts of the new mouse.

This is a chimeric mouse, with different cells coming from different origins, either wild-type or ABC123-mutant. I try to generate a number of different chimeras to breed together in the hopes that at least some of my original injected mutant cells went on to form the gonads, and the mutant gene can be passed on to its offspring. I then breed the various chimeric mice to WT mates in hopes of producing heterozygous offspring, which have one copy of the WT-ABC123 gene (from one parent), and one copy of the mutant-ABC123 gene (from the other parent). These mice can then be bred together to produce homozygous "double-knockout" mice, which I can then use to study my gene's effects and its possible relation to skin cancer. This is the type of animal typically sold by Jax, although this depends very strongly on the gene being studied.

Now, there are many issues that can arise along the way, such as the mutation being embryonic-lethal, causing sterility, or other defects that don't allow you to produce true knockout mice. Much can still be learned, though, and scientists have gotten very inventive in producing functional animal models of previously-difficult mutations. For example, it is possible to engineer a strain that only becomes a knockout when you feed it a certain chemical in its water, or is only knocked out in certain cell types or tissues. Some gene functions are only apparent when two (or more!) genes are knocked out at the same time. Genetics is incredibly complex, but fascinating, and more and more complex tools are being developed all the time to assist scientists in their research and ultimately help people overcome illness and disease.


Do cell membranes have more phospholipids in one layer than in the other? Assuming the cell membrane to have a spherical shape, geometry tells us that the area of the inner leaflet is smaller than the area of the outer due to the difference in radius between them. Does this mean that the inner layer has fewer phosholipids? And, if so, how does it affect the fluidity relation between the layers?

Yes there is a difference in the number of phospholipid molecules because of the curvature. This is very evident when there is a lot of bending as in case of exocytosis (see here) but otherwise I do not think there would be an enormous difference in the number of phospholipids between inner and outer surface of the bilayer.

Assumptions:

Cell is spherical
Cell diameter = 1µm (overall)
Thickness of bilayer = 6nm
Width of a phospholipid molecule = 1nm

Difference in circumference of outer and inner layers = 2π(6nm) ≅ 37.7nm

So approximately 37 more phospholipid molecules in the outer layer in this cross section of the cell. This is just 0.6% of total number of phospholipids in the outer membrane.

I don't think fluidity will be compromised because of this - only if a layer is overpacked will the fluidity be affected.


What is a sequencing artifact? I'm rather new to bioinformatics, so this might be a rather basic question, but what are sequencing artifacts, in the context of variant calling?

Artifacts are variations introduced by non-biological processes. Sequencing involves a lot of chemical reactions, and changes in nucleotides that can seem like mutations are really introduced somewhere in the processing of the sample. That's what we call "sequencing artifacts". Proper experiment design, with careful replication, should help you clarify which changes in nucleotides are biologically significant.


Why dogs move their noses when smelling? I read on Wikipedia that:

  The wet nose, or rhinarium, is essential for determining the direction of the air current containing the smell. Cold receptors in the skin are sensitive to the cooling of the skin by evaporation of the moisture by air currents.

That explains why their noses are wet. Why they're slightly moving them when smelling, like on this video (see the close-up in the second part)? Could this very little movement create enough air currents around the nose to determine what smells are coming from what directions? Or is there another reason?

The dog's ability to smell the world around him and to interpret these odors depends on a complicated chemical sensory system. First of all, it possesses mobile nostrils, that help to determine the direction of the smell. Then comes sniffing, the ability to disrupt the air with a regular pattern of breathing that, through laboratory testing, is structured in a series of 3 to 7 snorts. Most of the sensory organs of the dog's nose, the septal organ, are probably responsible for the outbreak of sniffing behavior.

The air is scented, it passes over a bony structure called "projection sub-ethmoid", that man does not possess, and nasal membranes that cover it. The area above the protrusion is not sweep, when the dog exhales air and it allows olfactory molecules to settle and accumulate.

When a dog breathes normally, air is introduced into the nasal passages, it continues its way to the lungs. The action of smell allows air to remain "at rest" in the nasal passages. The intricate complex surrounds the maxillo-turbinate bones of the skeleton provides that the nasal membranes are capable of creating models of air flows odors that lead content in the air to hit the regions of the olfactory receptors.

The odor molecules disintegrate and are concentrated in the nasal mucus that adheres to the receptor cells. Once the mucus, load odor, adheres to the microscopic hairs of receptor cells, the chemical signal odor turns into an electric signal and is sent to the cerebral cortex and the limbic system, ie, the part of the brain that regulate behaviors feeding, drinking and sex. Small molecules stimulate the olfactory nerve of smell. Big odor molecules stimulate the trigeminal nerve, one of the largest nerves of the skull, and the volatiles of sex hormones probably stimulate the vomeronasal organ, the other part of the anatomy of the dog that does not exist in primates.

http://www.ucsuggiatevedano.it/l-olfatto

EDIT @ kmm

Their nostrils can move, like the eyes to focus and channel the light energy. Or the highly mobile ears of many predatory animals, including cats and owls, which can rotate, also independently one from the other, not only to improve the perception, but also to identify the direction of the sound.

The principle is the same as the frontal binocular vision, which allows us to calculate the distance.

EDIT II @ terdon

When the dog sniffs, "taste" a smell with a series of inhalations shorter and faster than normal, as we do when we feel a bad smell, breathes quickly several times to understand what smell is that.
Of course we are well-educated people and we do not do this in public. But the gesture is the same. =-]

EDIT III @Petr

"Smell is the ability to detect and discern the odorous emanations from the air. The snuff is the ability to intercept and discern the odorous emanations from the ground. They act with a pattern of regular breathing and is structured in a series of one / three smells accompanied by a series of three / seven snuffs.
The behavior is controlled by the organs of sense of smell nasal septum."
(Section 3.3.3.4.1 and the following)

http://www.fongaros.it/ana2.pdf
http://www.cacciapassione.com/cani-e-cacciatori/1956-olfatto-del-cane-tutta-questione-di-naso.html

The dog is able to absorb the chemicals present in the air, thanks to the characteristics enjoyed by its olfactory cells. To further stimulate their sense of smell to the dog no choice but to expand with some emphasis their nostrils sneaking in a strong "suction" of odors. The air will be retained more or less long and the dog will recognize odors also very weak.

http://www.ucsuggiatevedano.it/l-olfatto
http://en.wikipedia.org/wiki/Olfaction

The nose of the dog is also called truffle, at its end there are the nostrils or the cavity, through which sucks air, and the vibrissae, equipped with sensory hairs. The dog's nose is particularly sensitive, is equipped on the inside of an organ said "of Jacobson", which allows to perceive any kind of substance, able to distinguish between a million of specific molecules, over that of perceiving pheromones, i.e. substances that indicate important information about the physical and mental state of others like it.

http://www.comeaddestrareuncane.com/blog/tag/cani-molecolari/

In the dog, the surface of the olfactory mucosa varies between 70 and 150 cm2 - in this tissue the number of olfactory receptors varies from 250 to 280 million - In 1962, Becker et al. showed that dogs are able to recognize substances in dilutions from 1/100 to 1/10.000.000.
- http://milano.corriere.it/milano/notizie/cronaca/12_febbraio_19/cani-olfatto-parere-esperto-1903358352720.shtml

Have you noticed how a dog sniffs the urine of a female "tasting it"? It is the same action that makes the viper when it follows the track of the mouse: it evertes the tongue and carries on it the odorous particles in the buccal cavity, and this organ has a function in the middle between the olfactory and gustatory ones. "Pointing dogs" is as pointing "the wild" taste the smell.
"Eat the scent", in the jargon, because savored, not only in terms of smell, the smell of the wild. The Jacobson's organ is then a second organ capable of perceiving odors, the first we've said is represented ciliated epithelium of the mucous membrane of the nose.
But there is a third organ called the "Rodolfo-Masera" which also serves to sense the emanations chemical (not yet known which), that way you could explain a specialization of these organs to perceive certain groups of biochemicals than others.
- http://www.laciotola.net/Cani/la-funzione-olfattiva-del-cane.html


Gibbs free energy and entropy in enzyme catalysis In enzyme catalysis, the formation of the enzyme-substrate complex causes a reduction in the entropy of the system. If entropy reduces, the gibbs free energy will become less negative. How then is enzyme catalysis favorable? Are there any other factors that off-set this?

As @canadianer hinted, the answer is enthalpy.

ΔG = ΔH - TΔS

For binding to be a spontaneous process ΔG must be negative. If the binding of a ligand to a protein decreases system entropy then ΔS is negative and the entropy term -TΔS is positive. However ligand binding involves the formation of various protein-ligand interactions (hydrogen bonds, ionic interactions, van der Waals interactions) all of which make a negative contribution to the change in enthalpy, so ΔH is negative. If |ΔH| > |TΔS| then ΔG will be negative.

This simplified account ignores the parallel changes taking place due to the ligand 'dissociating' from the solvent.