Confusion related to a term probe-by-background interaction I was reading a paper related to bioinformatics where it uses the drug response on the cancer cells and the gene expression of the individual cells are studied to find any useful insights. Specially, using the gene expression of the cells a predictor of the drug response is created.

They have stated that just using the correlation between the gene expression and the drug response might not be a good predictor. But the genes interact through signaling pathways to drive a particular drug response.

What these guys have done is like used PCA on the gene expressions of the cancer cells to use the components which preserve the greatest variance.

Actually, I didn't get what they mean by probe-by-background interaction and how it is calculated.

Can anyone please explain. I googled for a while but didn't get it.

Here are some quotes from the paper where the term is used

  Towards this end, we have compared how well drug response can be
  predicted by simple statistical models, which either directly relate
  probe and background networks to drug response or consider
  probe-by-background network interactions.

  To generalize this approach, the term ‘probe’ could be
  replaced by individual transcript expression levels measured through
  other gene expression methods. Similarly, ‘background networks’ and
  principal components are used interchangeably. Generally, ‘background
  networks’ could be represented by any data reduction method that
  summarizes the expression of a gene network. We demonstrate that
  probe-by-background network interactions significantly enhance drug
  response predictions, over and above the predictive power garnered
  through utilizing individual probes and background networks alone.

The "probe by background" interaction is the response of different probes as a function of background gene expression. For example, depending on which of the 6 backgrounds a probe is in, the drug response may go up or down. Probes as a function of background is probably easier to imagine than background as a function of probe (which is equally valid). For 39,115 probes and 6 background networks, there are 234,690 interactions.

In a technical sense, "probe by background" is the interaction term in the linear model that the authors fit for each drug. The details of the analysis are in the supplemental methods. The model they fit is

Drug_Response ~ Probe + Probe * Background + Background

which translates to "Drug response is modeled by Probe, the interaction of Probe and Background, and Background". The middle term (with the *) is the interaction term. Here is a page that helps to explain how to understand significant interaction terms in linear models.


What does a climax community lead to? Seral communities modify the environmental conditions in such a way that these are less favourable for itself and more favourable for the next community. Each community acts to end itself.

If the same is applicable to the climax community, what does it lead to?*

As pointed out by @bshane it seems your question is answered by the definition. From the relevant wikipedia articles

  "A seral community (or sere) is an intermediate stage found in ecological succession in an ecosystem advancing towards its climax community."

and

  "In ecology, climax community, or climatic climax community, is a historic term that expressed a biological community of plants, animals, and fungi which, through the process of ecological succession the development of vegetation in an area over time, had reached a steady state. This equilibrium was thought to occur because the climax community is composed of species best adapted to average conditions in that area."

It doesn't lead anywhere, it is the climax. It is the state a community reaches when there is little change in the biodiversity as it because the community is composed of species at proportions that suit the ecology well.

However, in reality it seems that climax communities are rarely (if ever obtained) and, with increasing climate change and habitat invasion by humans, few communities will be in equilibrium. The adaptive landscape varies in time and space, thus while a community may be well suited to the current environment, it may well be poorly suited to future incarnations of that environment and will be undergoing constant change. As such, the term "climax community" is somewhat obsolete with it generally referring to old or established communities rather than those at a climax.


What is the modern state of the theory of evolution? When I studied biology at my medical school, we used to learn topics around a century old: the famous Darwin's voyage on "Beagle" to the Galapagos Islands, the classical triad of his Theory of Evolution, etc.
At the same time we were told that there is no evidence found in nature for many of these statements of his evolutional theory. For example, people studied wildlife around Chernobyl and found that no new species emerged due to much higher mutation rate as a consequence of radiation. On the contrary, there were no significant differences between the species living under elevated radiation level and those living in "normal" conditions.
Do these facts somehow influence our understanding of the theory of evolution? Are there any breakthrough findings which happened in the last 20 years that prove or disprove it?

My friend Brightblades is right in one thing.  It seems your teacher was working off a caricature of what the theory of evolution actually says.  First of all, you should read Sklivvz's excellent answer at this question.  Now to address the elephant in the room, the accident at Chernobyl only happened in 1986.  That was only 26 years ago.  In that timeframe, noticeable effects in an animal population really would not be at all noticeable.  Furthermore, the paper cited by Marta Cz-C actually shows that there have been some changes (in fungi though, not animals).

  fungi seem to interact with the ionizing radiation differently from other Earth’s inhabitants. Recent data show that melanized fungal species like those from Chernobyl’s reactor respond to ionizing radiation with enhanced growth. Fungi colonize space stations and adapt morphologically to extreme conditions. Radiation exposure causes upregulation of many key genes, and an inducible microhomology-mediated recombination pathway could be a potential mechanism of adaptive evolution in eukaryotes.

Read the rest of the paper for more information on how there have been some other slight changes to fungi at Chernobyl as well as other locations throughout the world.

Now I am going to repeat a bunch of stuff from one of my web pages that talks about evolution.  This web page is set up mostly to deal with creationist arguments, however, the caricature is so severe as to warrant this.  As I said earlier, evolution is a population phenomenon.

Evolution acts upon heritable variation of characteristics, and you can only have variation of this sort within a population. A single individual organism, at least if its a multicellular eukaryote, has a fixed genome. It can't change what it has inherited. But a large number of organisms can all have different genomes, and can disseminate variation via inheritance to the next generation. It is upon the population as a whole that evolution acts, with various mechanisms coming into play to remove some variations from the population, and propel other variations to numerical dominance within the population. The organisms in question remain part of that population, and within a generation, those organisms don't change. But the moment a new generation is produced, dissemination of variation can result in the appearance of a new feature in one or more members of that population. If that new feature leads to greater reproductive success for the organism possessing it, that feature spreads through the population, as more and more future offspring inherit it. Over time, the population changes, and more and more organisms with new features appear within that population.

Understanding inheritance basics and mechanisms for changes (genes), we have all that is needed for the appearance of cladogenesis events. Split a decent sized population of living organisms into two, and let's call these new, separate populations A and B. Now let a barrier be erected between population A and population B, so that individuals from one cannot reproduce with individuals from the other. This barrier can be an insurmountable physical obstacle, for example, but this need not be the only form such a barrier can take. Now, first of all, there is no reason whatsoever to think that population A and population B will start off in identical states to begin with. After all, those two populations were derived from an original population comprising lots of organisms with different genomes, and the likelihood of population A and population B being identical at the start of this process is vanishingly small. Then, once our barrier is erected, and our populations are allowed to reproduce separately from that point on, there is no reason to think that those populations will move in the same direction in the long term. Indeed, it is far more likely that they will be subject to different environmental and ecosystem influences, and those different environmental and ecosystem influences will shape the long term heredity of those populations. Indeed, that's all that natural selection IS - it's a single, concise term used to encapsulate all of those environmental and ecosystem influences succinctly, and additionally to encapsulate the fact that those influences affect the inheritance of characteristics within a population over the long term.

As a consequence, any two separated populations of living organisms, that originated from a single population, will diverge from each other. If the extant influences on those two populations are sufficiently different, that divergence will take place more rapidly. Eventually, we will arrive at a point where those two populations become sufficiently diverged from each other that individuals from population A can no longer produce viable offspring with individuals from population B, and vice versa. When this happens, we have a speciation event. Indeed, this has been observed taking place in the wild AND in the laboratory, and has been documented in the relevant scientific papers. So, if anyone wishes to assert that there are 'magic barriers' to speciation or other cladogenesis events, then reality doesn't agree.

You will not have any animals giving birth to any radically different animals as a result of radiation.  Most changed sue to radiation will not provide any particular advantage to an animal anyway.  Also, a change may also be dependent on a previous change and require many generations to fully manifest.  All this was demonstrated by the long term evolution experiment led by Richard Lenski at Michigan State University.

So in essence, your teacher was just plain wrong.  As for the findings of the past 20 years, we are always learning more and more.  For instance, there has been an explosive capability in DNA analysis and sequencing, which has only provided more support for the theory of evolution.  A mechanism that Charles Darwin could not have had any idea about in his day and age, yet it perfectly supports his conclusions.  Again, read the answer provided at Skeptics.


Is missing Q wave characteristic for Wolff-Parkinson-White Syndrome? No my study books says about that no Q waves in WPW syndrome.
They are about wide QRS complex often however.
I heard today that the characteristic property of WPW is often a missing Q wave, like here

This is caused by the presence of an abnormal accessory electrical conduction pathway between the atria and the ventricles.
However, some books are about delta waves which is characteristic in the above picture.
However, it is many times very difficult to see.
These missing Q waves are however much easier when PRS complexes.

How much false positives do you get if you categorize all missing Q waves and PRS complexes as WPW syndrome?

How characteristic is the missing Q wave for WPW syndrome?

In Wolff-Parkinson-White syndrome, the normal Q wave is usually masked by the preexcitation action potential which produces the delta wave. Despite this, missing Q wave is not a diagnosis criteria of the syndrome, and up to 70 percent of the patients show a negative delta wave which causes differential diagnosis problems because it is confused with Q, according to Emergency Electrocardiography.

  When the delta wave is negative, this simulates a Q-wave. This is known as a pseudo-infarction pattern, and is seen in up to 70% of patients with WPW.

And this negative delta wave also helps in determining action potential origin, according to Medscape.

  A general rule is that Q waves (negative delta waves) point away from the earliest site of ventricular activation, which is typically the insertion point of the bypass tract.

No, you can't categorize PRS complexes as WPW syndrome. In fact there is no PRS complex. A classic ECG of WPW will show a shortened PR segment and a widened QRS (or RS or RSr' or however it looks) complex.


How close to Earth's core can organisms live? We don't to know much about organisms living deep below the Earth's crust. Recently a team led by S. Giovanni discovered some microbes 300 m below the ocean floor. The microbes were found to be a completley new and exotic species and apparently they feed off hydrocarbons like methane and benzene. Scientists speculate that life may exist in our Solar System far below the surface of some planets or moons. This raises some questions:

What is the theoretical minimum distance from Earth's core where life can still exist. Please explain how you came up with this number. For example, there are temperature-imposed limits on many biochemical processes.
Is there the potential to discover some truly alien life forms in the Earth's mantle (by this I mean, life which is not carbon based, or life which gets its energy in ways we have not seen before, or non DNA-based life, or something along these lines)?
What is the greatest distance below the Earth's crust that life has been discovered? I believe it is the 300 m I cited above, but I am not 100% sure.

There's a lot we don't know about life in deep caves, but we can bound the deepest living organism to at least 3.5 kilometers down, and probably not more than 30 kilometers down.

The worms recovered from deep mining boreholes are not particularly specifically adapted to live that far down: they have similar oxygen/temperature requirements as surface nematodes.

The Tau Tona mine is about 3.5 kilometers deep and about 60˚ C at the bottom. Hydrothermal vent life does just fine up to about 80˚C, and the crust gets warmer at "about" 25˚C per kilometer. It's entirely reasonable to expect life to about 5 kilometers down, but further than that is speculation.

Increasing pressure helps to stabilize biological molecules that would otherwise disintegrate at those temperatures, so it's not impossible there could be life even deeper. It may even be likely, given that the Tau Tona life breathes oxygen.

I am certain no life we might recognize as life exists in the upper mantle.


How to obtain bacteria samples at home? As the original question went from hold to closed, I thought I would write up a more appropriate question.

How should one go about getting bacterial samples to look at under a microscope at home?  How do professionals do it?  What if I want to look at cool pathogenic species like Salmonella bongori, Escherichia coli, or Bacillus anthracis?

First, and I cannot stress this enough, you should not go seeking out human pathogens if you don't have the appropriate equipment to handle it at the right safety level.  That goes for all pathogens, even ones you might find around your house.

In a professional lab, you might get samples from collaborators, clinical samples, vendor, or really an number of other professional resources.  A well respected vendor as an example is ATCC, but the general public wouldn't be able to "shop" there.

But you really don't need to go far to get a whole host of microbes to study, you can grow them all at your house.  The basics of bacteria culturing can really be broken down to three steps: (1) get a source of bacteria, (2) put some of the bacteria in an environment where they can grow easily, and (3) harvest them to do something useful with them.

(1) Is fairly easy, bacteria are everywhere.  You can swab nearly any surface of anything in your house and come up with microbes (note you might also get some mold/fungi).  In this case (3) is easy as well.  Once you have culture you can streak it across a slide to view it under a microscope (you could also use several proper mounting techniques).  After all, looking at microbes under a microscope is the real goal here!

The only part of this plan that will take some real elbow grease is making your own culture dishes at home, but it's not as hard as you might think.

Making your own culture dishes:

1) The "plates" themselves.

  I recommend getting the smallest Tupperware like containers your can
  find that are microwave safe, dishwasher safe, and really make a good
  seal (water tight at the least). They really don't have to be big, and
  you will make your life easier if you buy a bunch to match. They need
  to be super clean. After running them through your dishwasher at home,
  put them all in a boiling pot of water until you are ready to pour in
  your "medium." A mid-low simmer will work

Note that you won't probably be able to have perfect sterile technique at your house, but you should try to do what you can.

2) Your "Medium" or Broth

  I highly recommend using pectin as your gelling agent if you can't get
  your hands on some agar. After that comes plain unflavored gelatin,
  but I recommend pectin. You can get it at almost any grocery store and
  my recipe is made assuming that. You can determine how much you want
  to make, just scale up the ratios. I'm going to list things as rough
  volume by volume so you won't need a scale.

  i) Make the powder first:

  45mL of pectin;
  4 bouillon cubes ground as finely as you can (you can get different
  types and results depending on if you start with vegetable, beef, or
  chicken. I recommend starting with vegetable.);
  125mL of refined white sugar;
  Additives (more on this later)

  ii) Mix the powder into 500mL of water.

  Before you mix in the powder, heat the water to 50-75oC (mid low heat), but not boiling. Mix the powder in while stirring until
  dissolved.

  iii) Bring the mixture up to a boil. Let it boil for about 2 min,
  stirring all the while.

  iv) Cover the pot and let it cool for 4-5 min.

  You by no means want it to cool down to room temperature, you just want
  to get it a little below boiling. If you are at 55oC or below it's
  definitely time move on.

  v) Dip/fill your "plates" 1/3 full of media using clean/sterile
  utensils and seal while hot but not boiling.

  You may have noticed this seems an awful lot like canning, and that's
  because it is. Again you want to be as clean as possible in this step
  and of course try not to burn yourself on anything.

  vi) Let your media plates set and chill over night in the
  refrigerator.

  You really probably only have to wait a few hours if you are anxious
  to get going. You are going to want to store the plates that you are
  not using in the refrigerator anyway. Also if you made a bunch of
  plates, let the cool on a counter before you put them in the fridge so
  that you don't raise the temp of your fridge too much.

  Remember the thing about additives? You can play around with adding
  different amounts and different types of salts, vitamins, food, or
  other items to see how they affect the cultures you get to grow. All
  kinds of fun there. First go round, leave them all out.

Now you have your own home made culture plates! The above recipe was empirically tested by my childhood, and repeated by my son's. Not all pectin from the store may be equal, this is with Ball Classic (I have no relation to the company). I'd love to know people's results in trying it, because I might need to re-think how/what I'm doing to get it to work.

Go around your house swabbing things with sterile swabs (you can get these at a drug store), and then streak them out on plate. While it will be a little different with a swab and homemade plate, the idea is similar to what is done here.

Leave your plate in a warm wet place, but not in direct sunlight. Ideal temp is going to be around 37, but you can leave them above and below that and still get things to grow. On top of our dryer is where I leave them.

After a day or so you should have colonies you can streak out on a slide and look under a scope. You will find all kinds of things this way. If you want a more formal way to put things on a slide, you can check out dry and wet mounting from a Google search.

You are actually quite likely to run into E.coli if you sample enough "areas" this way. Obviously don't eat or huff the stuff that ends up growing. Maybe you can post some fun pictures of this if you try it.

As pointed out in the comments, if you successfully get bacteria to grow, then you will need to successfully get rid of them.  I should point that a good set of rubber gloves (that you can bleach and wash after use), or disposable gloves are a really good idea when handling plates that have grown bacteria.

Clean Up

First off, I want to clearly say that this stuff can clog a pipe.

If you tried to grow something on a plate, and you didn't get a colony that you can see with the naked eye (note some microbes might make CLEAR growths) you can probably just scoop the gel into the trash.

Note that I said probably.  If you swapped any part of your body, waste, or that of an animal you must decontaminate even if you didn't see anything grow.  On the plus side decontamination is easy.

If you did see something grow, or you otherwise need decontamination:

First make a 20% bleach solution in a large Tupperware like container (probably don't want to do this is a nice metal pot, but could do it in a junk one).  You can go as low as 10% bleach solution if you sure your bleach is NOT a cheap already watered down brand (like something bought at dollar store).  But just to be sure, I recommend 200mL of bleach in 800mL of plain tap water.

Drop your plates and lids into the bath (with the lid off) and let it sit for 10-15 min.  Then, working under/in the bleach solution with your gloves on, use a fork/spoon to get out the medium (it will be like thick jello).  Do this for all your plates, and you can do more than one at a time this way.

Once you have all the medium out and floating in the bleach, take the plates out and put them in the dishwasher.  Strain out the bleach/medium/funkiness you grew through a cheap colander (I recommend dishwasher safe plastic like PP).  Put what get's caught in the colander in the trash and take the trash out.  Wash the plates, lids, colander, and large container you used for the beach bath.

Slides

Slides present extra caution because they can break or shatter to create sharp edges.  For the most part, if you cover your sample with a cover slip, and seal it with nail polish, you can actually keep your slides indefinitely with little risk.  If you do decide to dispose of them, they should first go into a thick Ziploc bag (use an expensive freezer guard type bag for this) or into a Tupperware you don't mind throwing away.  If you never sealed your sample to your slide, you should also decontaminate the slide in bleach first (as above, with extra caution to not cut yourself).

If you are sophisticated enough to get microscopic photos of the microbes you see, by all means post them up and we'll try to ID them as best we can (many look very similar, and we use genetic or protein markers to get a true ID).


Chaos theory and population cycles of odd periodicity I have just begun to read about Chaos theory and have come across the statement that "Period three implies chaos."

My question: Does any odd period imply chaos or only 3? If so, how can populations of cicadas that cycle every 17 years exist?

The chaotic behaviour you are referring to (at least the one described in your link in the comments) is a property of the discrete version of the logistic equation, where you get chaotic dynamics at growth rates above ~3.55 (see the logistic map). The behaviour of this equation has been described in a classic paper by Robert May (1976). As you increase growth rate (a in your link) from one you go from a stable attractor (approached directly or by dampened occilations) to cycling behaviour (between 2 to 4 to 8 states as growth rate increase) to chaotic dynamics, which is shown in this bifurcation diagram.

And to be clear, nothing of this has anything to do with period/cycle length per se (in the sense of species interactions or lagging feedback loops), but is a property of the model and the population growth rate. The statement about period 3 implying chaos probably refers to a brief window around r ~3.83 ($1+\sqrt{8})$ where you get cycling between three values, and at higher values then this you only find chaotic behaviour (which you get at lower values as well though).

Addition:
I now realize that the statement "Period three implies chaos" comes from the theoretical paper with the same name (Li & Yorke, 1975). This paper proves that all one-dimensional models (not only the equation above) that has a period 3 cycle will also show chaotic behaviour. This proof is a special case of the Sharkovsky's theorem, which is older but was unknown to Li & Yorke at the time.

There is also a question at MathSE that deals with the same problem, and some of the answers there link to useful resourses:
https://math.stackexchange.com/questions/2901/period-of-3-implies-chaos


Why is the liver the only internal organ of the human body to regrow? Related to my earlier question, "How does the human liver regrow?", am curious as to why the liver is the only major organ that has this capability?

Why is it that other major organs, such as the heart and lungs etc are not able to regrow in the same fashion?

Maybe it is due to two factors:

The liver is one of the few solid non-tubular organs. If a tubular organ is damaged, all the layers that composes it must regenerate. This layers usually have different cell types, which is always nasty for regeneration since some of them may be formed by specialized tissue (for instance, myocytes are very difficult to regenerate. If the organ has a muscle layer, such as the esophagus, regeneration will be more difficult). Furthermore, damage in a tubular organ usually involves perforation, which will disrupt its function even if the injure isn't big.
Hepatocytes are pretty undifferentiated cells. They are basically enzymatic sacks with some vacuoles and mitochondrion, but they remain as your typical animal cell. They have a regular nucleus, they don't have any cytoskeletal adaptation and their vacuoles don't compose the most part of their cytoplasm (in a healthy liver). Cells with so little morphological specialization usually regenerate with no problem. Plus, the liver itself is constantly exposed to chemical damage due to toxins, drugs and other chemical compounds that may be present in the diet. This situation is special and don't apply for any other organs, with the exception of the kidneys (which, in fact is a very complicated tubular organ).


How do omega-3 fatty acids reduce cholesterol at the molecular level? I have heard that omega-3 fatty acids found in fish are a good way to prevent/reduce cholesterol problems.

My question is how do omega-3 fatty acids do that: what are they doing on a chemical level to produce this effect? And is there any way to maximize this effect through other substances, that may work in concert with them?

I found this research paper (pdf) by D. Roger Illingworth, William S. Harris, and William E. Connor (Journal of the American Heart Association, 1984) that offers some help. Its abstract says:

Diets rich in omega-3 fatty acids derived from fish oils lower the plasma concentrations
of low density lipoproteins (LDL) and very low density lipoproteins in humans. The present study was designed to examine the mechanism(s) by which diets enriched in omega-3 fatty acids reduce plasma LDL cholesterol levels in normal subjects.

In the Dicussion part, you will find your answer:

Reductions in the plasma concentrations of LDL in human subjects consuming diets rich in long-chain omega-3 fatty acids from fish oils or omega-6 fatty acids from vegetable oils may be due to a reduction in LDL synthesis, an increased fractional rate of catabolism of LDL, or a combination of both... The present study indicates that the hypocholesterolemic effects of long-chain omega-3 fatty acids present in fish oils results from a reduction in the rate of LDL apoprotein B synthesis and that such oils do not stimulate the fractional rate of catabolism of LDL. These observations imply that the incorporation of omega-3 fatty acids into cellular or lipoprotein lipids does not enhance the rate of receptor-mediated catabolism of LDL as has been observed with omega-6 fatty acids in vitro.

I could not find a paper on its exact mechanism, so I'd rather say that the process is still not clear. Yet, as the paper suggests, the main effects of omega-3 fatty acids are reducing LDL synthesis and/or increasing fractional rate of catabolism (FRC) of LDL.
A similar article can be found here:

Omega-3 fatty acids have been shown to lower triglycerides, which are a type of fat in the bloodstream. Experts aren't sure of the exact mechanism. Omega-3 fatty acids may also slow down the growth of plaques in the arteries and reduce inflammation throughout the body.
A number of studies going back years have shown the benefits of fatty fish. In an important review of studies, researchers found that getting daily omega-3 fatty acids from fish oil could lower triglyceride levels by 25%-30%. The results were published in The American Journal of Clinical Nutrition in 1997.

BUT, I would also like to point out that the question itself "omega-3 fatty acids found in fish are a good way to prevent/reduce cholesterol problems" seems to be a matter of debate because of articles like this:

New data presented this week provide clues as to why eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA)--both components of omega-3 fatty acids--have differential effects on LDL cholesterol.
Presenting the results of the laboratory study here at the National Lipid Association (NLA) 2011 Scientific Sessions, senior investigator Dr Preston Mason (Brigham and Women's Hospital, Boston, MA) said that EPA is an inhibitor of lipid oxidation at normal and elevated cholesterol levels in the presence and absence of DHA, while DHA seems to have no real effect on lipid peroxidation. This trial was one of a number of studies that attempted to address the clinical question as to why LDL-cholesterol levels increase in patients treated with the triglyceride-lowering omega-3 fatty acids. In his trial, Mason et al compared the effects of EPA and DHA--alone or in combination with statins--on lipid peroxidation in polyunsaturated fatty-acid– and cholesterol-enriched vesicles.


What is the mechanism of monofunctional glycosylases? I am learning about the base excision repair mechanism. I understand generally how glycosylases work, but I am trying to understand this with much more detail. I found a paper where they write:

  Monofunctional glycosylases catalyze the single-step displacement of damaged base via attack of an activated water molecule on c1' of the substrate.

I am not sure what an activated water molecule is and how, for example, an aspartate residue is making a water molecule 'activated'. Furthermore, how is this activated water molecule hydrolyzing the N-glycosyl bond to remove the damaged base. Thank you for any help.

The article referred to in the question is Fromme et al. (2004). I was able to find several proposed mechanisms for the monofunctional uracil-DNA glycosylase but I'll discuss two that seem most relevant in the context of your question.

The first I'll mention was outline by Parikh et al. (2000) who studied recombinant human mitochondrial uracil-DNA glycosylase. They report a mechanism where the glycosidic bond cleavage is not induced by a nucleophilic attack by water but rather by valence electron rearrangement, induced by conformational changes of the substrate by the enzyme, leading to a resonance stabilized oxocarbenium intermediate. This figure shows an electron pushing representation as well as the various stabilizing effects produced by orbital overlaps which favours cleavage of the C-N bond:

  Original caption: Structure-based reaction mechanism that resolves the apparent orthogonal paradox for electron transpositions by altering the substrate stereochemistry. (A) A simplified valence-bond representation of the glycosylic bond dissociation hides the paradox that the three electron pairs to be transposed are involved in orthogonal orbitals. (B) In the normal anti-conformation of deoxyuridine, the σ*-orbital involved in the anomeric effect and the π-orbital of the C2⩵O bond are orthogonal to one another, thus preventing orbital overlap. (C) Severe distortions of the deoxyribose and the glycosylic bond in the strained conformation of deoxyuridine enforced by the UDG active center align the pairs of atomic orbitals participating in each electron transposition, thereby electronically coupling the anomeric and σ-πArom effects to promote bond cleavage.

They also go on to say (emphasis added):

  A water is tightly positioned 3.54 Å below the deoxyribose C1′ by four hydrogen bonds (Fig. 3B) but is likely a poor nucleophile. Instead, the UDG–DNA substrate structure suggests this water is well positioned to become the 1′-α-OH after dissociation of the incipient deoxyribose oxocarbenium ion from the uracil ring.

Here is Fig. 3B from the article, where the water molecule is the red sphere at the bottom of the image coordinated by four hydrogen bonds:

The next mechanism involves a nucleophilic attach by an activated water molecule and was outlined by Drohat et al. (1999) studying Escherichia coli uracil-DNA glycosylase. Here is the first step of the mechanism:

  From the Wikipedia article on uracil-DNA glycosylase (accessed 15 Jul 2014)

Drohat et al. (1999) describe this:

  UDG apparently follows a [...] mechanism by deprotonating the incoming water nucleophile using the completely conserved residue Asp64 as the general base. Site-directed mutagenesis studies of the human enzyme support the structural evidence that His187 and Asp64 act as a general acid and base, respectively, because conversion of these groups to leucine and asparagine resulted in 300- and 2500-fold losses in activity (11). However, structural and mutagenesis data alone cannot establish the catalytic roles and ionization states of active site groups; thus other complementary approaches must be utilized to establish a chemical mechanism.

To answer your question, the water molecule is considered activated because it is a better nucleophile due to proton abstraction by the aspartate residue side chain. Thus the electrons used in in the original O-H bond in water (which are polarized towards the electronegative oxygen) are free to attack the partial positive 1' carbon of the deoxyribose. Although it is a concerted mechanism, you could perhaps think of the nucleophile being the hydroxide anion, which is much stronger than water.

So which mechanism is correct you might ask. Well, I don't know, but I refer you to a paragraph from Parikh et al. (2000):

  Despite the importance of UDG and the many proposed mechanisms for its catalysis of glycosylic bond cleavage, the structural chemistry underlying efficient catalysis by UDG has remained elusive. Two groups, including our own, have proposed a traditional acid-base catalysis carried out by a cationic His-268 and an absolutely conserved Asp-145 (13, 26). Two proposals (27, 28) invoke only general base catalysis via the same catalytic aspartate and a neutral histidine. Another proposal (29), based on a computationally simulated uncleaved-substrate complex, predicts that Asp-145 is fully solvated in the substrate complex so that it cannot act as a general-base catalyst. These proposed mechanisms are inconsistent with each other and with the uncleaved-substrate crystal structure presented here. Moreover, they are problematic in that they rely entirely on functional group chemistry and thus do not adequately explain UDG's efficiency or the activity of mutants that alter evidently key functional groups (13, 27). UDG mutations that remove apparently key active site functional groups are actually faster enzymes than several wild-type DNA glycosylases (30). Thus, without knowledge of a substrate complex structure, the characterization of UDG mechanism is severely hindered. Here, we present the structures of UDG bound to both uncleaved-substrate analog at 1.8-Å resolution and cleaved-product DNA oligonucleotides at 2.0-Å resolution. These high-resolution cocrystal structures suggest how UDG applies part of the DNA-binding energy to glycosylic bond cleavage by conformationally altering its deoxyuridine substrate to take advantage of stereoelectronic and strain effects in what is then an apparently dissociative process.

References:

Drohat AC, Jagadeesh J, Ferguson E, Stivers JT. 1999. Role of electrophilic and general base catalysis in the mechanism of Escherichia coli uracil DNA glycosylase. Biochemistry-US. 38(37):11866-11875.

Fromme JC, Banerjee A, Verdine GL. 2004. DNA glycosylase recognition and catalysis. Curr Opin Struct Biol. 14(1):43-49.

Parikh SS, Walcher G, Jones GD, Slupphaug G, Krokan HE, Blackburn GM, Tainer JA. 2000. Uracil-DNA glycosylase–DNA substrate and product structures: Conformational strain promotes catalytic efficiency by coupled stereoelectronic effects. P Natl Acad Sci USA. 97(10):5083-5088.


What are 'factors' in biology? My question is what does the word 'factor' mean in words like transcription-factor or nerve growth-factor? What is similar between these different compounds such that they deserve the word 'factor' in their name?

Edit: My confusion comes perhaps from the use of the word 'factor' in statistics, where it refers to a variable that can take on discrete values (e.g., the factor Gender takes on values 'male' and 'female'). Here a different meaning of the word seems to be used.

There are many meanings of "factor" in Biology. In the context where you place it, namely bio-active substances, such as hormones and enzymes I would go for the definition given by the Medical Dictionary:

  factor [fak´ter] :
  an agent or element that contributes to the production of a result.

Within this definition, a transcription factor contributes to the transcription of DNA into mRNA, and nerve growth factor contributes to the growth and survival of neurons.


Will ammonia continue to accumulate in an aquarium tank if a strong antibacterial or chlorine is added to the water? I've always wondered what would happen if dead plants and fecal matter lay in chlorinated waters and/or waters treated with strong antibacterials or antibiotics.

I've heard that aquarium tanks owners warn against using strong antibiotics as it can kill nitrifying bacteria which convert toxic ammonia to a safer form of nitrate. Otherwise, ammonia levels can buildup and be toxic to the aquatic life in the tank.

However, that doesn't make sense to me. Even if the nitrifying bacteria die, wouldn't the ammonifying bacteria which produce ammonia in the first place also die? Would there be greater amounts of ammonia in the water after these agents are repeatedly used, or would ammonia levels with nitrate levels together fall significantly?

A very large part of the bacteria and fungi will die so very few biological prosesses will continue in the tank if you add chlorine or antibacterial chemicals.

Ammonia will slowly outgass from the water oxygen and CO2 will reach equiriblium in the water as little oxygen is used and little CO2 is produced,it is the same with the other atmospheric gasses.

Life in the tank will simply stop until the toxins are broken down or removed,by toxins i mean chlorine and/or antibacterial chemicals.

Nitrate level will not change as little is produced and little is used,any denitrification will stop too.

denitrification can only happen in an anaerobic environment but denitrfying bacteria too are killed by chlorine and antibacterial chemicals.


Does the light color spectrum and frequency matter for photosynthesis? Do plants grow differently when given sun light, wolfram lamp, fluorescent light, LED light, infrared, ultraviolet, x-ray, unfocused laser and stroboscope?

It matters a lot.
Take a look at this graph:

This graph is for the "normal" plants containing chlorophyll.

There're also "abnormal" :-) ones, simple water plants and cyanobacteria, that contain various phycobilins for photosynthesis instead of the chlorophyll.

If your question is practical, I'd recommend using specialy-designed fluorescent lamps called grow light.


Skull mystery on beach The skull was found on a beach on the Sechelt inlet on Canada's pacific coast. A marine environment.

What species is this skull from?

We found a very similar skull on a beach near Richardson Bay, Lasqueti BC. Decided it was a seal skull (locals agreed)
See harbor seal skull: http://www.skullsunlimited.com/record_species.php?id=4726


Genetic variation in humans and model organisms (measured by SNPs) I was wondering what is the range of SNP density across species and model organisms.

I.e., what would be a reasonable estimate for the SNP density (i.e., x SNPs for each 1 Kb) in:

humans
humans with the highest variation (i.e., Africans)
flies
mouse
lab mice with highest variation (i.e., isogenic lab mouse 1 with isogenic lab mouse 2 with the highest variation)
model organism with the highest snp density (could be lab or naturally occurring)

SNP Density

Human = ~1.18 SNPs per kbases

  Based on CgsSNP, the average numbers of SNPs per 10 kb was 8.33, 8.44,
  and 8.09 in the human genome, in intergenic regions, and in genic
  regions, respectively.

Source: Investigating single nucleotide polymorphism (SNP) density in the human genome and its implications for molecular evolution. by Zhao Z, Fu YX, Hewett-Emmett D, Boerwinkle E.

Drosophila melanogaster = ~0.02 SNP per kbases

  FLYSNPdb provides high-resolution single nucleotide polymorphism (SNP)
  data of Drosophila melanogaster. The database currently contains 27
  367 polymorphisms, including >3700 indels (insertions/deletions),
  covering all major chromsomes. These SNPs are clustered into 2238
  markers, which are evenly distributed with an average density of one
  marker every 50.3 kb or 6.6 genes.

source: FLYSNPdb: a high-density SNP database of Drosophila melanogaster

Mouse(Mus musculus) = ~0.2 SNP per kbases

Source: Genome-wide single-nucleotide polymorphism
analysis defines haplotype patterns in mouse


What is the core mechanism behind neuroplasticity? Specifically I am looking at reopening of the critical period of plasticity.

Modern neuroscience has started to unlock the secret of neuroplasticity.

A common experimental setup is with mice. They have a critical period between days 20 and 32 when they learn binocular vision. And if you cover one eye during this period, they never learn to use it properly. Covering the eye even for extended periods outside of this window has no long term effect.

Scientists can then test out various plasticity hypotheses. And they had indeed found several mechanisms that can restore binocular vision to adult mice.

You can find a list towards the bottom of this paper: Autism -- A 'Critical Period' disorder?

enzymatic degradation of PNNs
SSRI
HDAC inhibitors (which are suggested to knock out Nogo-66 receptor)
AcetylCholineSterase inhibitors

It is suggested that there is an underlying pattern of excitation/inhibition (E/I) balance that all of these 4 techniques perturb.

Where can I read about this E/I balance in detail? The Wikipedia page on NeuroPlasticity (here) appears to be a dead-end.

I am looking for an overview, rather than technical scientific papers that explore a particular aspect, already assuming familiarity with the big picture.

How to get the big picture?

EDIT: T K Hensch seems to be a world leader in this research, and his papers answering my questions, for example http://www.ncbi.nlm.nih.gov/pubmed/24439367

This is a good first source which suggests further references:

http://www.scholarpedia.org/article/Balance_of_excitation_and_inhibition


Advantages of pain sensation? The hazards of congenital insensitivity to pain (CIP) are well-known.

This question is about the obverse: what selective advantage, if any, does the normal sensation of pain confer? I'm thinking of severe pain such as that associated with back injury, burns, and some intestinal problems in which the pain seems to serve no function other than to incapacitate.

A related question is whether there is a spectrum of sensitivity to pain, ranging from CIP to heightened sensitivity, what the distribution looks like, and whether this is a genetically plastic trait (like color perception)? If the distribution were sensitive to selective pressure then naively I would guess it serves our needs well, but we spend a lot of our collective time trying to dial it back, hence my question.

Yes a range of pain exists. This can be seen probably in your friends who all probably have a completely different threshold for pain. When doctors ask patients to rate their pain it's usually to establish a baseline so after treatment we can see if there's a decrease. The different thresholds have so many factors from general health to receptors to brain activity to emotional state. You name it! Often just focussing on a pain makes it more painful.

It's definitely an unpleasant sensation pain but it's our way of our body saying "hey, you need to pay attention". Usually the response required is rest or to identify what might be there causing the pain. For example pain means we will withdraw very quickly from a hot surface. Doesn't even require the brain as it is a reflex arc which minimises the time we spend burning that part of our body. And as it continues to hurt we use the arm less letting it recover and protecting it from infection by doing so.
As these hazards of being cut, burnt, bit, knocked, fractured are very common there is a survival advantage to be the individual that is alerted to these hazards and take the necessary actions. Particularly in children where pain is necessary as it makes the baby know it needs to eat (or the mother) or that something isn't a good idea (putting hands on something hot).

However as you say there are times when the pain itself is more crippling than anything else and in that situation we have a problem. Childbirth, backache and in cancer or in tension headaches are just some examples. As being able to feel pain is pretty much required for a long life, the disadvantage of having pains like the above is less and doesn't outweigh the benefits. Pain is always going to be necessary. They also usually don't interfere with reproduction and so genes are passed on.


When something "smells moldy" what are we really smelling? When things smell moldy --  it could be clean clothes left in a heap, a damp basement, old books stored in elevated humidity -- they can smell moldy.

There are distinct smells for each of these.

Are we smelling the mold spores themselves, or are there other molecules released by molds that causes the "moldy smell" we perceive?

The vast majority of the things you smell are odorants, or volatile molecules; not spores. They are light compounds that have high vapor pressure (are airborne), and that interact with your chemoreceptors in your nose (can be smelled). The most-often reported microbial volatile organic compounds in living environments according to this study are as follows:

2-Methyl-1-propanol
3-Methyl-1-butanol
3-Methyl-2-butanol
2-Pentanol
3-Octanol
1-Octen-3-ol
2-Octen-1-ol
3-Methylfuran
2-Hexanone
2-Heptanone
3-Octanone
2-Methylisoborneol
2-Isopropyl-3-methoxy-pyrazine
Geosmin
Dimethyl disulphide

Geosmin is probably the most moldy-smelling and is detected very sensitively by olfactory systems of animals that want to avoid contaminated food. To me it smells muddy, or earthy, like soil after a rain shower. In our lab, about half the people find it a pleasant smell. It can be smelled in wine, it's the earthy taste found in vegetables, it's the smell of dead bacteria, and so on and so on. The term petrichor describes the odor and geosmin is a major contributing odorant for this.


From inflammation to sickness and depression: when the immune system subjugates the brain Recently, some research, for example this article has proposed that inflammation can cause innate immune cells to produce pro-inflammatory cytokines that act on the brain to cause sickness behaviour.

My questions are:

(1) What medication would potentially help to reduce the inflammation? I am not a biology expert so I do get a little confused reading the research articles.

(2) What are cytokines in laymen's terms? Are they the same as histamines which cause allergies?

Cytokines are essentially signalling molecules of the immune system. Broadly speaking these can be classed as pro- or anti-inflammatory. Pro-inflammatory cytokines promote inflammation, and anti-inflammatory cytokines inhibit inflammation.

Inflammation (again, broadly speaking) is associated with the 'innate' immune response - this is the immediate response by neutrophils and macrophages (among others), and these cells release a variety of molecules designed to damage cells around them. This is great if those cells are bacterial, or damaged host cells that need removing, but not so great if that is 'normally' functioning tissue.

Aging is associated with increased systemic inflammation - i.e. a greater proportion of pro- to anti-inflammatory cytokines. The causes of this aren't entirely certain, but it could be that the adaptive immune response (i.e. the memory T-/B- cells) is not as effective in older ages so the innate response is more important, or that it is just simply left 'unchecked'. Either way, the result this that the pro-inflammatory response can end up damaging host tissues, including the brain, without the corresponding repair instigated by anti-inflammatory cells/cytokines.

Any anti-inflammatory medication (e.g. aspirin, ibuprofen, or glucocorticoids) will, in theory, reduce inflammation, but by suppressing the immune system the risk of infection naturally rises, and there may be unforeseen consequences to prolonged use (the immune system does a lot more than just fend of bacteria - e.g. it is essential for tissue maintenance and regeneration), so I am by no means suggesting the use of anti-inflammatories to protect brain function!


Determining sequence of oligoribonucleotide Oligoribonucleotide X was treated with phosphatase (for removal of 3'
  and 5' - terminal phosphates), then with RNAase T1, which cleaves all
  phosphodiester bonds located in a 3' position of guanosine in a
  5'-specific manner.

  As a result, oligonucleotides L, M and N were generated in equal
  amounts. Each of them was further treated with phosphatase and
  subjected to alkaline hydrolysis. Results are listed in the table
  below.

  Then experiment was modified: oligoribonucleotide X after treatment
  with phosphatase was hydrolyzed with RNAaseP, which cleaves all
  phosphodiester bonds in a 3'-position of pyrimidines in a 5' -
  specific manner.

  This hydrolysis yielded five products in approximately equimolar
  concentrations: uridine monophosphate, cytidine monophosphate and
  oligonucleotides P, Q and R. After resolution of the mixture and
  alkaline hydrolysis of these oligonucleotides data listed in the table
  below were obtained.

My thinking : G can not be at the 5' end otherwise we would get a single Guanosine also in the first experiment. G can also not be at the second last from 3' end as we have not got any singles. We have got A and C in a duplet and so they must have been at the 3' end.

I also have trouble understanding the significance of "mole/mole of oligoribonucleotide".

I am trying to fit  in other results but am unable to do so.
A GOOD HINT WILL BE APPRECIATED MORE THAN A DIRECT ANSWER.

Thanks

Here are a few hints which might help you:-

1) You get free UMP and CMP (in contrast to UMP + C or CMP + U) in the second experiment before alkaline hydrolysis.

2) There are two CMP in "N" oligoribonucleotide, and a free cytidine (and not CMP) in "M" and "Q".

3)Use the fact that all oligoribonucleotides were treated with phosphatase before being subjected to alkaline hydrolysis.

(Referring to your comment, I dont know why do you think consecutive cytidine is not possible).

These are a few hints that helped me solve this. If you want further clarification or the answer, tell me in the comments.

Answer for reverse derivation:- $5'-UACGCCGAC-3'$


If my brain lost all of its activity for a moment, would my memory be gone too? I can't remember which question it was, but in the past here, it was explained to me that memory is actively stored in the brain, rather than "physically". Meaning, memories are made up of the brain's activity, not its physical cell structure.

I'm not sure I have that right though. I mean, that, for one thing seem inefficient and overly complex. It seems like a vast amount of energy would be required to store so much information in the form of activity patterns. Maybe I misunderstood. So I'm asking. If my brain lost all of its energy (activity) for a moment (for example, one second), would my memory be gone too?

Memories are dynamic; that is not equivalent to "memories are evanescent". Cellular structure and composition controls memory, not just a continuous passage of signals. This point is already discussed in the comments.

Loss of energy (in the form of ATP) would cause memory deterioration and in some cases neuronal cell death too— strokes, which happen due to lack of blood supply to brain (and hence unavailability of nutrients and oxygen) can cause amnesia.

But one second will practically not affect anything.


Is dextrocardia congenital? Dextrocardia is displacement of human heart to the right side. Does it occur during the life span of a human being or right from birth?

As the comments pointed out, this is not a hard question to answer with some research, but I'll add a few more details.

Dextrocardia is congenital. The human heart normally actually isn't so much on the left side - it's more pointed towards the left. In dextrocardia it points more towards the right side. This develops within the first few weeks of embryonic development, as the heart is one of the first organs to develop.

Source

It occurs in about 0.7 percent of live births and 2.7 percent of stillbirths, indicating that there are health problems in the fetus associated with it. After birth, it's possible that the heart functions perfectly fine, but often there are other heart defects associated with dextrocardia.

Dextrocardia with situs inversus is a condition in which the heart and visceral  organs are reversed. As for the cause, it's genetic and follows a recessive inheritance pattern, meaning both parents need to be carriers, but don't necessarily have the condition.


What causes bacteria to change their proteins to become resistant to antibiotics? FMRSA (meticillin-resistant Staphylococcus aureus) became resistant to penicillin by a change in its DD-transpeptidase. What triggered this change? Did it happen by chance or does the bacterium have some sort of response mechanism to cause this change on detecting penicillin?

The bacteria doesn't know.

When an organism copies its DNA, it sometimes makes mistakes. Different organisms have different rates of making mistakes; the rate of mistakes can be really high in some organisms like bacteria.

DNA copying mistakes (or unintended changes without copying, like due to UV damage) can sometimes be a big problem for multicellular organisms. If some of your cells have different DNA than others, they might function poorly, or they might grow too fast, stealing the space and nutrients from other cells in the organism, causing cancer. Multicellular organisms like humans have a lot of DNA repair mechanisms and methods to detect DNA damage and have cells sometimes suicide when they have been damaged.

For bacteria, DNA copying mistakes aren't as much of a problem, and there are lots and lots of bacteria out in the world. That means a lot of different mistakes. When a mistake is bad for a bacterium, it is more likely to die. Those types of mistakes therefore don't get recopied over and over again.

Sometimes a mistake is accidentally helpful.

Occasionally, a mistake actually makes a positive difference for an organism. If there are trillions of bacteria, just a few of them might have mistakes that make them resistant to a particular antibiotic. Let's say it's 1 out of 1,000,000,000.

In normal conditions, that doesn't matter much. If it doesn't hurt them at all, they will just keep on replicating the mistake, and other bacteria keep on replicating no mistake, and the proportion stays 1 out of 1,000,000,000.

Accidentally helpful mistakes become more common in a population

Now, let's say you expose that population to antibiotics that kill 99% of the bacteria with no mistake, but kills none of the bacteria with the mistake. Now, your 1,000,000,000 bacteria is 10,000,000 bacteria, but you still have 1 with a mistake. Now when those bacteria replicate, 1/10,000,000 will have the mistake. If they grow evenly back to 1,000,000,000 now you have 100/1,000,000,000 bacteria with the mistake. As you repeat this process, eventually you will have lots of bacteria that have the mistake, and that proportion of individuals will be insensitive to the antibiotic.

Biologists call these mistakes "mutations" and they call the increased survival and reproduction of organisms with helpful mutations "natural selection" - over time, natural selection is an important contributing factor to evolution of species.

At no point in this process is any awareness of what's happening necessary! All you need is variation, caused by replication mistakes, and some selection pressure that gives an advantage to individuals with certain mistakes. Making some mistakes in replication is a constant source of variation in biology, and the key process that, along with selection, has led to the vast variety of life around you.


Could someone recommend an introductory book on epidemiology? I'm hoping to learn the basics of epidemiological methods, terminology, etc. I come from a background in statistical economics, and I'm moving into the economics of public health. I don't know if epidemiology uses separate statistical methods, but I presume it does. I know discussion questions aren't recommended, but please list any reasons you have (personal experience, ease of introduction, etc.) for texts you would recommend.

There are two books I'd highly recommend for someone starting to dabble in Epidemiology. The first is Kenneth Rothman's Epidemiology: An Introduction, which I'm affectionately going to refer to as "Baby Rothman" from hereon out for reasons that will become obvious.

Baby Rothman is an excellent "getting your feet wet" book. It's simplistic, and clearly designed for someone with no background in Epidemiology, so it starts from things that, if you have a statistical background, you might find a bit dull. But it accomplishes two key tasks:

A basic treatment of the subject from a pre-eminent methodologist and advocate for the field that doesn't make some of the sloppy slight-of-hand mistakes many introductory books do.
An introduction to the "vocabulary" of Epidemiology as a field - what we call things, how we thing about effect estimates, etc.

The second book I would buy would be Modern Epidemiology: 3rd Edition by Rothman, Greenland and Lash. This is the definitive reference book for most epidemiological methods  currently used in the field. As I said on a related CrossValidated question, ME3 is the only epidemiology book that has always come with me, regardless of what project I'm doing, and which I have routinely found invaluable.

The other benefit of the book is that it's "platform agnostic". It's not going to try to teach you a statistics package - its going to teach you the science and philosophy of Epidemiology, the actual doing of the science, rather than the toolkit. Without that kind of methodological rigor, you can be a wizard at your language of choice and still do bad science.

If I were only going to buy one book, it would be ME3.


Soft and Hard selection Seems to me that these two sources (M. Whitlock, B. Wallace) use different definitions of soft and hard selection.

M. Whitlock: Soft selection occurs when the relative fitness of an individual is calculated relative to the fittest individual of the local patch. Hard selection occurs when the relative fitness of an individual is calculated relative to the fitness of the fittest individual in the whole metapopulation.

B. Wallace: Soft selection occurs when the relative fitness of an individual is calculated relative to the fittest individual in the population. Hard selection occurs when the relative fitness of an individual is calculated relative a hypothetical fitness. Therefore, extinction only occurs under hard selection but never (except eventually when all individuals have fitness of 0) in the soft selection case.

Are there other definitions? What is the most common definition?

I think Wallace (1968) developed the ideas of hard and soft selection, as they relate to genetic load. He further explains the concept in Wallace (1975). As the idea was his, I'd go with Wallace's definition over Whitlock's.  I haven't had time to watch the Whitlock video to see if they are saying more or less the same thing overall.

Consider a hypothetical population of individuals, each with 1000 loci (I'm basing example and ideas on an example given by Ridley 2004, pgs. 162-167). Heterozygotes at each locus has the greatest fitness (heterozygote advantage). Homozygotes at any locus will have reduced fitness. Therefore, the fitness of each genotype is given as:

AA: $1-s_{AA}$

Aa: $1$

aa: $1-s_{aa}$

Even if every individual in the population at time zero was heterozygous at each locus, Mendelian inheritance ensures that no individuals will be heterozygous at all loci after the second generation.  Assume that fitness reduction at each homozygous locus is just 1%. Given that well over half of the loci will be homozygous, fitness of those individuals will be reduced to 0. They will die before reproducing.  This is hard selection.  If hard selection of this magnitude occurred in a population, then extinction would occur. This is what Wallace (in your link) is saying.  This mortality due to the genetic load is added to the normal background mortality.

Soft selection compares the fitness of an individual to the genotype with the greatest fitness in the population, even if that genotype does not the theoretical optimum fitness. Soft selection replaces some of the background mortality with selective mortality, so the population size is not decreased overall.

Literature Cited

Ridley, M. 2004. Evolution. 3rd ed. Blackwell Publishing, Malden, Massachusetts, USA.

Wallace, B. 1968. Polymorphism, population size, and genetic load. pp. 87-108 in R.C. Lewontin, ed. Population biology and evolution. Syracuse University Press, Syracuse, New York, USA.

Wallace, B. 1975. Hard and soft selection revisited. Evolution 29: 465-473.


How does your body ultimately recover from a cold? Is it the eradication of the virus (assuming rhinovirus) by white blood cells? Or does your body somehow adapt to presence of the virus?

Great question.
Rhino Virus
For the rhinovirus in particular, it is eradicated.
Integrase
However for some of the retroviruses and other virus that contain an enzyme called 'integrase', they actually integrate their DNA with yours. That way as your cells go about their business, they make the virus genes too. However, you have some white blood cells called CD8 T Cells that mark these 'compromised cells' for death.
Evading
Some viruses though can remain cleverly hidden and don't turn on their own genes in your genome until the immune response goes down, or you stop taking anti-retroviral drugs.  HIV is a great example of a virus you can also 'live' with but never actually eradicate. The medicines you take can kill all the circulating virus down to a non detectable level. However, when you stop taking your meds, the DNA integrated in your genome will start making the virus again, thus you will always 'live' and can never eradicate it.


What characteristic(s) of inverse agonists allow for inhibitory effects? I know that inverse agonists have similar structure to its complement agonist; and, as a result, they have the ability to bind to the same receptor, causing an inhibition of the pathway considered.

My question is, if the agonist and inverse agonist have the same structure (and possibly/extremely likely the same energy levels, steric effects, etc.), how is it that the receptor molecule reacts differently?

The short answer is that an inverse agonist binds preferentially to the inactive state of the receptor, so it reduces the receptor's intrinsic, basal activity. The agonist was only raising the activity, not switching it on.

The most basic model of receptor pharmacology is that the receptor, $\ce{R}$, and the agonist, $\ce{A}$, are in a chemical equilibrium: $\ce{A}+\ce{R}\rightleftharpoons\ce{AR}$. In this model, the agonist bound receptor, $\ce{AR}$, generates the biological response. But in truth, this isn't a very accurate model since nothing's actually happened to the receptor. Why should $\ce{R}$ generate a biological response when it's bound but not when it's unbound? This model also wouldn't explain inverse agonists.

The del Castillo Katz model rectifies this problem by suggesting that there are two equilibria. The first is for agonist binding. And the second is for a conformational change in the receptor to an activated state, $\ce{R}^*$, that causes the biological response. Hence, $\ce{A}+\ce{R}\rightleftharpoons \ce{AR} \rightleftharpoons \ce{AR^*}$. This activated state is a different shape of the receptor, which allows a biological response. Depending on the receptor type, it could be an opened ion channel, a 7TM protein which destabilises the binding of a G-protein or more.

For many receptors (such as the GABAA receptor), the receptor can go into the active, $\ce{R^*}$, state without an agonist being bound. Hence we have the equilibrium $\ce{R}\rightleftharpoons \ce{R^*}$. This is called constitutive activity - the receptor generates some level of biological response by itself. So this shows us the chemical properties of inverse agonists. An inverse agonist binds with a higher affinity to the $\ce{R}$ form of the receptor than the $\ce{R^*}$ form. So the equilibrium shifts to the left and the receptor has reduced constitutive activity. So the drug reduces the biological effect by pulling it below the basal level. See the figure below: figure 3-1 from (Blumenthal and Garrison, 2011). NB: they opt for $\ce{R_i}$/$\ce{R_a}$ instead of $\ce{R}$/$\ce{R^*}$ and $\ce{L}$ for a generic ligand.

An agonist and inverse agonist definitely don't have the same structure otherwise they'd be the exact same molecule. They might have the same pharmacophore but they necessarily have some chemical difference that makes the inverse agonist prefer binding to $\ce{R^*}$ but not the agonist. To be honest, I'm not convinced that they even need the same pharmacophore. Although as far as I know in most cases, they do. It's not too difficult to imagine a situation where the conformational change from $\ce{R}$ to $\ce{R^*}$ moves residues in a binding pocket and prevents (sterically/electronically) the inverse agonist from binding as easily. I'm not so sure how the energy levels would work here so you'll have to get back to me on that or ask the chem/phys stackexchanges.

My crude figure below has a 7TM protein (Green) with a G protein (brown) attached. The receptor can undergo a conformational change to the $\ce{R^*}$ form (horizontally flipped) which causes the G protein to dissociate and cause some biological effect. The agonist (red star) can bind into the pocket but fits with a much higher affinity for the $\ce{R^*}$ form since the conformational change gives it a nice binding pocket. Since it fits better in the $\ce{R^*}$ state, the equilibrium shifts to the right so the G protein prefers to dissociate and the agonist introduces a biological effect.

On the other hand, the inverse agonist may fit better into the $\ce{R}$ binding pocket than the $\ce{R^*}$ binding pocket. Hence, it shifts the equilibrium to the $\ce{R}$ state, so the G protein prefers not dissociate and the biological effect is reduced.

Further reading: (Blumenthal, D. K. and Garrison, J. C. (2011). 'Pharmacodynamics: Molecular Mechanisms of Drug Action' in Goodman and Gilman. 12th ed. The Pharmacological Basis of Therapeutics) and ( Rang and Dale. (2015). 'How drugs act: general principles' in Pharmacology. 8th ed.)


Help identifying what this is in Crayfish gills? this is my first time posting here. I was in my Zoology lab doing a dissection on a Crayfish when I noticed these hairlike structures within the gills. They were very "snappy" and fine, and would break off if I pulled hard enough. I put some on a wet mount under a dissecting microscope, but my Lab prof and the parasitologist could not identify it. We put it under a compound microscope and thought maybe it is an animal but we couldn't definitively say it had no cell well. My profs thought it was an animal, with setae, but I would really like to know what it is

Edit here are the images:

My best guess would be Trematoda which is a fluke worm that infects mollusk. I would think this is the larval stage of cercaria which is free swimming and develops in the mollusk and then moves on to infect others.

Here are some different images of a cercaria:

In this YouTube video you will see what is known as a "Rat King" which is just a ball essential of Trematoda. Here is a screenshot


Do fallen leaves produce oxygen? After a leaf has fallen from a tree, if it is still green and hasn't dried out, is it still converting CO2 into O2 if not put in water?

Can anyone find any data showing how long any different species of leaf will continue to produce oxygen after fallen?

Short answer
It all depends on the time window you are talking about. After having been detached from the mother plant, a leaf will typically keep on photosynthesizing for a few hours or so.

Background
Cutting of the stalk of the leaf results in impaired water flow and wilting. As soon as a leaf is detached from the plant, it will also be cut off from hormones, minerals and other nutrients. The result of this is that senescence (and death) sets in straight away. However, leaves will typically stay green and moist for hours or even days, dependent on the conditions it is stored. Hence, in practice, photosynthesis can be measures at least a few hours after a typical leaf is picked (source: Science and Plants for Schools).


Does bioluminescence communcation occur on macroscopic level? Some bacteria are known to communicate using bioluminescence (quorum sensing). Do we observe the same phenomena in any macroscopic species?

Almost certainly. In the deep-sea, some species of laternfishes (Myctophidae) show sexual dimorphism in their light organs. Males have large light organs. The females are much smaller. Here is a brief summary, based on an interview with Dr. John Sparks at the American Museum of Natural History.

Sparks is discussing his recent publication with colleagues (Davis et al. 2014) that suggests that bioluminescent communication may actually facilitate speciation in some deep-sea fishes.

There are probably more instances of communication using bioluminscence in deep-sea organims but, to my knowledge, the Davis et al. paper provides the best evidence so far.

  Davis, M.P. et al. 2014. Species-specific bioluminescence facilitates speciation in the deep sea. Marine Biology 161: 1139-1148. (open access)

On land, Stoltz et al. 2003 has demonstrated that positive selection has acted on bioluminescent color in Jamaican click beetles. The male beetles use the flashing to attract females for mating. Some males emit yellow light while males in a separated area have orange light.

  Stoltz, U. et al. 2003. Darwinian natural selection for orange bioluminescent color in a Jamaican click beetle. Proceedings of the National Academy of Sciences USA 100: 14955-14959.


Amplification technique for proteins similar to PCR for DNA? I know PCR can be used to amplify a tiny sample of DNA in order to perform experiments. Is there a similar technique to use on a protein sample? More specifically, I'm not interested in "cutting" up the protein but simply making more of the original sample.

There isn't any technique with one exception. PCR generates DNA from DNA so you can establish cycles. For protein synthesis, an mRNA is a template to produce proteins. Most likely proteins you are interested in would not synthesize mRNAs, so that you can not establish cycles.

The exception I said earlier is Protein Misfolding Cyclic Amplification (PMCA). Some disease associated misfold proteins can induce misfolding of the same polypeptide which is not misfolded. So you can establish cycles of misfolding reaction.

PS:

There are technique to synthesize proteins from DNAs or RNAs, but they are not chain reactions.
https://www.promega.com/products/protein-expression/eukaryotic-cell-free-protein-expression/
https://www.neb.com/products/e6800-purexpress-invitro-protein-synthesis-kit


Has any scientist elaborated on the "selfish neuron" hypothesis? Daniel Dennett references a talk by Sebastian Seung, where the latter speaks about "selfish neurons". I've been trying to learn more about this hypothesis, but cannot seem to find anyone who has elaborated on this line of thinking. Could someone point me to some resources, or this an idea whose time has not yet come?

I would argue that the "selfish neurons" idea is a lot less interesting in terms of biological implications than the similarly-named "selfish gene" hypothesis.

It's basically proposing a bottom-up understanding of neuronal circuits where the developmental design feature is that neurons are individually optimizing their input-output relationships in some way. There isn't really any biological controversy about this suggestion.

Dennett (and probably others) goes a little crazy with it and turns it into a discussion of the agency of individual neurons, etc, but from a biological perspective I would argue that this is a pretty boring type of agency, at least in so far as using this definition pretty much all cells in a biological organism would be argued to have agency, because they are on some level "making decisions," but that's all biology is: organic systems of machines that respond in some way to their environment, and which are subject to selection pressures by which the systems of machines that reproduce best come to predominate.

Where this argument is useful, and Dennett uses this approach as well, is in contrasting biological systems with silicon computers. However, all of today's machine learning algorithms are really based on "selfish" nodes according to Dennett's description.

In summary, the selfish neuron hypothesis is just a philosophical approach to what we already know about biological neurons. It's meant as a way especially for people from a more algorithmic/computational background to think about how biological neural networks differ from algorithms structured from logical first principles. It doesn't make strong hypotheses for biology beyond what is already understood and agreed upon. I think this is probably why you don't see much more study about it.


Time lapse between fresh blood's exposure to air and that same blood turning darker red-brown For investigative purposes, I'm searching for a tool that can be used as a quick visual assessment of the the length of time that blood has been exposed to air after the blood flow has stopped.. Let's say that you walk into a room and see someone unconscious. Where blood appears, it had already stopped any fresh flow & has already dried to a dark brown similar to mahogany wood.  That person has been there longer than how many minutes? Please understand that I'm not asking how long the person has been lying there but for at least how long?

You come upon a dazed person unsteady on their feet with an injury to the face. The blood flow has stopped: the person may have smeared the blood when touching their face but you  see that the blood has not changed to a deep brown and still retains a bright red color..approximately how much time has likely elapsed between the injury occurring and your encounter with the injured person?

I know there's no exact time estimate possible without testing but simply for quick field assessments, is anyone willing to hazard an opinion?

In summary: How can I tell the age of a blood stain?

In comments it been discussed that clotting is partial answer to OP. I would say, that is is somewhat tangential to the original question.

If I may re-phrase, OP asks: how one can estimate age of blood that has been exposed to air? Problem is that you will have to have a starting point to solve that backwards, like having an initial condition for solving differential equation.

One example that can be used is measurement of $pCO_2$ content in blood serum. If it is available, someone already collected this data. In 2 hours $pCO_2$drops 30% and total $CO_2$ drops about 6%.

Moreover, it seems that during hemorrhagic shock RBC shape changes, which means that sampling patient you will be able to approximate time since bleeding started. However, you will need an electron microscope at your disposal...

Finally, and I'll leave it like that, cellular death is a powerful process that leaves a lot of traces. Apoptotic cells have mitochondria bursting (except in RBC there are no mitochondria) and releasing, for example, cytochrome C. In case of bleeding probable cause of cellular death is necrosis, so different biochemical changes will occur. Point is that you can measure time since necrosis/apoptosis started by careful measurement.


Is T7 promotor leaky in DH5 alpha? In my experiment I found that a GFP gene under T7 promotor in high copy number pTAC-2 vector is showing green fluorescence producing colonies of DH5 alpha under UV light. what could be the possible reason?

Consider the phenomenon of zygotic induction, as originally observed by Art Pardee, Francois Jacob, and Jacques Monod (sometimes called the "PaJaMo", or "PaJaMa" experiment): regulation of a repressed promoter can be affected by the copy number of the promoter in the cell. Put another way, if the copy number of the lac operator in the cell is high enough to bind or titrate all of the available lac repressor protein in the cell, then some of the lac promoters in the cell will be expressed.


Does human organism consume water or is it only used as solvent? Dune (novel) describes a body suit called Stillsuit:

  a stillsuit is a "body-enclosing garment" of Fremen design which
  performs the "functions of heat dissipation and filtering bodily
  wastes", as well as retaining and reclaiming moisture

For this question, I am interested into reclaiming property of this suit. The book argues about the fact that the losses were virtually only due to exposed skin.

However, I am wondering if the human body is actually consuming (through biochemical reactions) any water or it is used entirely as a dissolvent or maybe as a catalyst), so that its loss entirely depends on the ability of reclaiming it externally.

Question: Does human organism consume water or is it only used as solvent?

Humans and all other animals actually are net producers of water ("metabolic water") by oxidizing sources of energy including fats, proteins, and carbohydrates - effectively the opposite of the chemical reactions that photosynthetic plants use to turn water and atmospheric CO$_2$ into biological materials and oxygen gas. There are also many metabolic reactions in humans that consume water (in particular hydrolysis reactions), but it is less than the amount produced.

However, water is indeed important as a solvent, and there are non-negligible losses through evaporation (especially when sweating) and an important role of water in the kidneys to assist in flushing waste.

If one was able to reclaim all evaporative losses and excretion losses, no additional water would be necessary. However, the energy requirements to do so go up exponentially the closer you get to 100% reclaimation.

The International Space Station has several water recovery systems to reduce the incredibly expensive cost of supplying enough water for humans on long missions in space. These systems include both urine purification and atmospheric reclamation but they do not approach 100% capture.


Why did scientists think humans had 100,000 genes (before the Human Genome Project)? One of the major results of the Human Genome Project (HGP) was that humans have far fewer separate genes than previously thought. From a 2004 article about the HGP:

  Francis S. Collins, director of the National Human Genome Research Institute (NHGRI), said, "Only a decade ago, most scientists thought humans had about 100,000 genes. When we analyzed the working draft of the human genome sequence three years ago, we estimated there were about 30,000 to 35,000 genes, which surprised many. This new analysis reduces that number even further [to 20,000-25,000] and provides us with the clearest picture yet of our genome."

What was the old estimate of 100,000 based on? I assume that in 1994 no one had sequenced the entire proteome...

As Remi.b points out, the 100,000 gene estimate may be based on the one gene–one enzyme hypothesis. If that's true, did people before the human genome project think that there were 100,000 distinct enzyme activities? If so, what experiments/data were used to establish that number?

Human genome is 3.2Gbp (giga=billions of basepairs). If you assume there are 100k genes, this yields around 32kbp (kilo=thousands base pairs) per gene.

Before human genome project, let's say before 1990, people were isolating a lot of genes from human-derived tissues. You can use google scholar to find relevant papers. From quick search, you can see that range is pretty large:

"186,000 base-pair (bp) human factor VIII gene"
"human TF gene spans 12.4 kbp"

So you can see how one might guess "average" size of the gene to be somewhere around 30kbp, if you haven't yet found too many genes. Whereas after genome sequencing, we know that genes are 100-10000 bp long. I think the issue was that there was no enough statistics yet to judge appropriately "average gene size". And as it turns out, the distribution is very funky. You need to isolate a lot of genes to reconstruct that distribution.

By the 1990 phenomenon of the alternative splicing was already known. What perhaps wasn't quite obvious, is how many genes there are, what their real sizes, and how many genes are overlapping


Cause of Crease in Drupe Fruit What causes the crease through the pericarp of a drupe fruit (peach, nectarine, olive)?  It may just be in exocarp as @Ilan pointed out, but I assumed (perhaps wrongly), that the division continued through the pericarp.  I'm also not sure if this true generically for drupe fruit, so I'm not sure which phylogenetic step down to take.  Olives for example have a divot that seems to extend from the stem down, but it stops well before the midline of the fruit in most cases.

I assume the crease has something to the initial genesis of the fruit tissue, but I haven't found any arguments on it's formation.  A more technical term might be "cleavage," but that was after some searching and not coming up with more certain term.

Botany is not my strong suite, but I recently entered into a collaboration where we will be making some recombinant alpha viruses (which is within my strong suite) that will infect drupe tissue.  Finding good pathology papers has been difficult, and they tend to be specific (not trying to imply that's bad).  Can anyone point towards a reference text/article on the genius of drupe fruit if the cause of the "crease" is not clear?  Disruption of the crease seems to be a particular phenotype of infection for some strains, and I'm searching for the correct terminology and mechanisms that might be effected.

If I can get permission I will include photos of an infected vs control peach.  In the mean time to clarify what I mean, the line that seems to transverse from one poll to the other of the fruit:

Peach:

Nectarine:

On the sea mango it is pronounced, but on most other mango it seems like just a slight marking along the exocarp:

Even the coconut seems to have at least one:

The structure you are relating to is a seam (suture). This seam is formed during development of a carpel.

The indentation of the seam varies and depends on the climate and environment: for example, water stress will give a very deep suture -


Is H antigen considered as an agglutinogen? A and B antigens which have the potential to cause agglutination in certain cases are called agglutinogens. But, as far as I know, H antigen cannot give rise to agglutination. So can it be said that H antigen also is an agglutinogen?

H antigen is a precursor for A and B antigens, and hh (recessive) individuals do not express this antigen. See Bombay blood group. This is an example of epistasis. Since H antigen is present in all A,B,AB and O blood groups, transfusion from any of these to an hh individual will cause a haemolytic reaction. Anti-H antibodies are agglutinins and have been referred to as agglutinins in the scientific literature.

  The fairly strong anti-H agglutinins present in 'Bombay' and
  'para-Bombay' individuals (see 5.5.6) are generally accompanied by anti-A and anti-B, neither of which can be separated from the
  anti-H specific antibodies.

   Schenkel-Brunner, Helmut. Human blood groups: chemical and
  biochemical basis of antigen specificity. Springer Science &
  Business Media, 2000. e-Book ISBN: 978-3-7091-6294-1


Why is the pituitary gland located in the brain? Why is the pituitary gland located in the brain in humans, instead of elsewhere in the body? Why would this be an evolutionary beneficial adaptation?

The evolutionary pressure on the location of the pituitary is likely not the reason why it resides at the basis of the brain. Instead, its (partly) neural origin makes it anatomically (and functionally) part of the brain. Why would it migrate out of the brain when it doesn't have to? What would the evolutionary pressure be on increasing the length of the axons connecting it to the other parts of the brain? It is part of the brain, hence it is located there. It clashes with the principle of parsimony to have the pituitary evolve to a structure located farther from the brain.

The neuroanatomy of the pituitary is schematically as follows (Fig. 1):

Fig. 1. Pituitary gland. Source: Imagekb.

The posterior lobe of the pituitary gland consists largely of extensions of processes (axons) from the hypothalamus and are part of the neurohypophyseal system. There are neural connections to the brain and other centres of the hypothalamus. Hence, the posterior lobe is neural tissue.

The cells constituting the anterior lobe of the pituitary gland are embryologically derived from an outpouching of the roof of the pharynx, known as Rathke’s pouch.


Raising two legs together while lying on bed Let's do some exercise(duh!)

Ok so lie on the bed. Lift your left leg. Put it down. Lift your right leg.Put it down. Easy?

Now lift your left leg and without putting it down, lift your right leg. Easy ? No.

Now try to lift both the legs together. Easy ? No.

My question : What is the anatomical reason ( arrangement of muscles around the bones etc.) which makes it difficult ?

I suspect it is just physics. Each of your legs makes up about 1/6 of body mass, leaving about 2/3 of your mass superior to your hips.

Raising one leg requires action of the hip flexors (i.e., iliopsoas complex) but also activity in the anterior abdominal wall muscles (rectus abdominis, obliques) and back muscles to stabilize your abdomen. To raise the other leg simultaneously, you recruit the ipsilateral hip flexors. But, importantly, you probably have already maximally recruited most of your abdominal and back muscles.

Imagine the body as a lever system. With one leg raised, you have 1/6 of body mass balanced against 2/3. With both legs up, you have 1/3 vs. 2/3 and with potentially increased torque, because your legs are long (a force acting at a larger distance). The muscle forces to stabilize that must be larger, but the additional muscles are not there.

I can raise both legs with difficulty (admittedly, $n=1$).


Haidinger's brush: Is this a by-product of the eye's physics, or are there any evolutionary grounds for it? The human eye is, very subtly, sensitive to the polarization of light. This is  an effect known as Haidinger's brush (see Wikipedia article of this name).

What, if anything, is known or at least intelligently speculated about the evolutionary "grounding" for this effect?

Another way to put this question: Some cephalopods and the mantis shrimp have sight that is sensitive to polarization of light and this sense is clearly begotten by evolutionary forces as it helps these animals detect prey and predators. So, is our subtle ability to perceive polarized light a leftover from a genetic forebear that benefitted from this ability? Or is it simply an artifact of the physics of the eye? The physics of Haidinger's brush is quite different from the topology of retinal cells that confers this ability in cephalopods and others I have read about.

A second question and related is: what is our nearest common genetic forebear that is known to exploit polarization sensitivity of its sight?

According to the link you provided, the phenomenon Haidinger's Brush seems to be associated with the macula of the retina. The yellow color of the macula may explain the yellowness of Haidinger's Brush. This suggests to me that the brush may be an artifact of the structure of the eye, and others have claimed that Haidinger's brushes probably do not have any ecological significance (Greenwood et al. 2003). If the brushes do not have an ecological significance, then they are very unlikely to have any evolutionary significance.

The brushes may be visible to other primates, such as Macaques (Snodderly et al. 1984), as they have a macula structure very similar to the human macula. This leads me to think the phenomenon would also be potentially visible to other primates such as chimps and gorillas. If so, then our nearest ancestor (forebearer) that could potentially see the brushes would be the common ancestor of humans and chimps.

For a broader review of polarized vision and underlying evolutionary hypotheses, the paper you linked to by Cronin et al. (2003) is a good review. I also came across a book, Polarized Light in Animal Vision. Polarization Patterns in Nature. by Gábor Horváth and Deszö Varjú and published by Springer. The front matter and table of contents are available here.  It appears to be a very thorough review of polarization vision in animals.

Literature Cited

Cronin, T.W. et al. 2003. Polarization vision and its role in biological signaling. Integrative and Comparative Biology 43: 549-558.

Greenwood, V.J., et al. 2003. Behaviorial investigation of polarisation sensitivity in the Japanese quail (Coturnix coturnix japonica) and the European starling (Sturnus vulgaris). Journal of Experimental Biology 206: 3201-3210.

Snodderly, D.M., J.D. Auron and F.C. Delori. 1984. The macular pigmnent. II. Spatial distribution in primate retinas. Investigative Ophthalmology and Visual Science 25: 674-685


Glass petri dish to replace plastic petri dish? I never use a glass petri dish before, but I just wonder if I can use it to replace for plastic petri dish because it can reusable. The only thing I worry is , in a Fridge's user manual, it said that do not put glass container into the freezer (usually -20 oC) because it can be damaged/break and even explode. So do a glass petri dish have any special design to prevent this damage?

Glass labware is usually made of borosilicate glass which is resistant to temperature changes, so putting a glass petri dish in a -20°C freezer should not be problematic, at least with respect to glass cracking because of temperature changes. I think the warning on your freezer is probably meant to warn against closed glass containers filled with liquid; as water freezes it expands and may mechanically break the glass, but for a petri dish is should not be an issue.

I would be more cautious about heat shocks with a -80°C freezer, though; in my experience at that temperature there is still a risk if the glass is not of good quality.

On a side note, depending on what you use the petri dish for, the surface chemistry  may be different from the polystyrene of plastic petri dishes, and if you are growing cells directly in contact with the surface, switching to glass may change their behavior.


Does the number of base pairs between the end of one gene and the start of the next gene have to be a multiple of 3? I'm working on a project for a Coursera course where I need to scan a string of base pairs and identify possible genes, but there's something about real DNA that I need to know to design the algorithm correctly.  My question is best illustrated by example.

Suppose we have a strand of DNA like this : ATGxxxyyyzzzTAAqqATGrsssATGuuTAAvpppTAG

The lower case letters just stand for general base pairs that are not in the sequences "ATG", "TAA", "TAG", or "TGA".

"ATGxxxyyyzzzTAA" constitutes a gene for the purposes of the assignment, and my program does correctly identify that string of base pairs as a gene. What I want to know focuses on what happens after that first gene is found. Let's consider the last portion of the string:

"qqATGrsssATGuuTAAvpppTAG"

My current gene-finding program would identify "ATGrsssATGuuTAA" as a gene, but notice that this strand starts after only two base-pairs ("qq") have been searched through. Does that matter? I.e., would this happen in real DNA, or should the second valid gene be identified as "ATGuuTAAvpppTAG"?

There absolutely is not a rule saying that all genes on a strand should be in the same frame.

Your program is looking for ORFs (open reading frames) and it should identify all of them, in every frame.  If you were being very thorough, you should generate the reverse complement of your sequence, and search that for ORFs too.  But I guess if you were given this sequence, presuambly the professor gave you the sequence in the desired orientation.


What is the H+ gradient in mitochondria? I would like to understand what the term H+ Gradient means. I googled this question and found terms such as chemiosmosis and ion gradient being tossed around. I am very new to biology and I do not know any advanced terms or anything of the like. What I do understand is that the mitochondria produces ATP and has something called a proton pump.

Thank you in advance.

Lets start with a general definition: A gradient is the difference in the concentration of a substance (this can be a solutant in liquids, a gas or whatever) between two places. The image below shows the general definition. If nothing else happens what keeps the gradient stable, over time diffusion will cause an equilibrium between both places. The flow of substance always goes from the high concentration to the low (indicated by the arrows).

In biological systems the two parts of the gradient are usually divided by a membrane and are more stable. Gradients can be generated by active transport which requires the input of energy to work against the gradient. Examples would be the concentration gradient along a membrane like protons (positively charged hydrogen-ions), as this can be seen in the mitochondria. Here three complexes of the respiratory chain (I, III and IV) pump protons from the matrix in the intermembrane space, which requires energy. The fourth complex (V) pumps the protons back and uses the released energy from this process to make ATP. See the figure below which shows this process schematically (from here):


Why the genome is divided into several chromosomes and not just a single big chromosome? In many eukaryote species, there are several chromosomes. In humans, for example, there are 23 pairs of chromosomes.

Why are there several chromosomes and not just a join of all chromosomes into a single big chromosome?

The leading contender of "why" in my former lab, is that if a chromosome becomes too long, a cell cannot fully isolate the chromatid to a daughter cell. Ie in a giant chromosome, the chromosome arms trail so far behind centromere, that the arms are of two sister chromosome are still touching each other even through the centromere have reached the opposite poles of a dividing cell. This prevents nuclear reformation. It would also mean, that the size of the cell will determine the chromosome maximum size.

At present this is a hypothesis. We have only just created the method to make ultra large synthetic chromosomes. I expected an answer is 3-5 years (2021-2023). However we say there is nothing special to a chromosome number.