cell biology - Example(s) of reduced rate of mitotic progression?

Most species complete mitosis, and in particular the process of chromosome condensation, rather quickly, in a matter of minutes. Are there any known species that undergo mitoses with substantially reduced kinetics (on the time scale of hours), particularly with respect to the processes of chromosome condensation (prophase through metaphase) or decondensation (anaphase through telophase)?

evolution - Systematic difference of diversity between sister taxa?

Bond and Oppell address your question points one, two and three empirically by looking for what they call "unbalanced bifurcations" as a sign of adaptive radiations in a well-resolved phylogenetic tree (spiders), and find that the number of unbalanced bifurcations does indeed exceed what they would expect to occur by chance.

As you mention and as I suggested in the comment, there are some serious problems that arise in trying to answer your question. Many of these are well presented in Cracraft, including assuming that higher taxa are comparable with one another, making arbitrary choices about what rank of taxa to compare, ignoring counterexamples, and qualifying rather than quantifying diversity. I think that Bond and Oppell effectively address most of these problems through rigorous, apriori definitions.

There's a diversity of opinions and evidence from biological systems on your fourth question point. Bond and Oppell connect these significantly unbalanced bifurcations to key traits (like orb-weaving) that open up new adaptive zones. I suppose therefore they might say that there's a fundamental factor (a key trait, and therefore open adaptive zones) driving diversification, and therefore might not agree with you that diversification would necessarily beget more diversification (at least, not in the absence of open adaptive zones). For instance, in Hawaiian tetragnathid spiders, ecomorph niches on an island are filled either through immigration from another island or through adaptive diversification (Gillespie). No ecomorph is represented by two sympatric species, so a niche filled by immigration will presumably not spur adaptive radiation. However, species radiations in Andean lupines (Hughes and Eastwood) and plethodontid salamanders (Kozak et al) seem not to have been accompanied by any key traits or particular ecological opportunity, and could theoretically be driven by the self-reinforcing mechanism you propose. As a related point, I suppose more diverse lineages could be less likely to go extinct; which could support diverse lineages becoming more diverse.

---

microbiology - How to obtain bacteria samples?

To be honest, you really shouldn't be buying such things if you're not prepared to handle them properly. If you work with a proper lab, you will be inindated with vendors trying to sell you these and many others.

But to answer your question, if you are looking to purchase many such items ATCC is an excellent resource. Not only will you have to meet regulatory requirements, but you will also have to deal with a great many MTA's depending on what you are trying to get.

In response to edit: Salmonella is actually not normally a serious pathogen to a healthy adult. It is, however, still a human pathogen and should be handled under BSL2 conditions. So if you have the funds and time to setup a BSL2 lab at your house, by all means go to town. And I hope you don't live with any children, the elderly, or otherwise immunocompromised individuals.

In response to further edits:
If you just want to look at things under the scope, then I suggest you get started by making your own homemade culture plates. If you can get your hands on some Lysogeny Broth (LB), agar, and petri dishes then you can make lb plates like a researcher in a real lab (minus an autoclave but you could use a pressure cooker). These are items the public could get, but might be harder to come by.

I however will assume that you want to make your own plates from common household ingredients (I used to do this a lot as kid, whatever that says about me).

**

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 "media." 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 "Media" 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:

  
  
  

  1. 45mL of pectin;

  
  

  2. 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.);

  
  

  3. 125mL of refined white sugar;

  
  

  4. Additives (more on this later)

  
  

  ii) Mix the powder into 500mL of water

  
  
  
  1. Before you mix in the powder, hear 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 cool down to room temperature, you just want to get it a little below boiling. If you are at 55oC or bellow 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 effect 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.

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.

microbiology - Factor causing Methicilin-resistance in MRSA?

I think you can normally think about similar pressures leading to extended-spectrum beta-lactamase (ESBLs) and methicillin/oxacillin-resistant Staphylococcus aureus (MRSA).

Going to the core of your question:

"Currently, the reported mechanism of methicillin resistance in S. aureus is the production of a distinctive penicillin binding protein 2a (PBP2a), which exhibits low affinity toward β-lactams"

But to really read on it you need to back to Liu et al.

Again Todar's is a great source for a good broad reading on staph including MRSA.

Response to Edit [inclusion of full question]:

TSDR: The answer is C.

Let's break down the three options given in the question and learn about MRSA along the way.

a. its MIC is increased to methicillin, but not to penicillin

First, for people who may not know, MIC is short for minimum inhibitory concentration. Simply, the MIC is a basic measurement of how much of any given agent is need to stop the growth of a bacterial colony. Often we think of current medical antibiotics when thinking of MIC, but even simpler things like table salt and sugar have a MIC for a given species. Thus this sentence is making the assertion that the bacteria found in the patent have an increased resistance to methicillin but not to penicillin. This leads us to ask the obvious question:

Can Staphylococcus aureus (staph going forward) be methicillin resistant but not penicillin resistant?

This is a bit of a trick question, but let's break it down to the needed components: What is Methicillin, what is/are penicillin(s), and how are staph resistant to them.

First that it should be noted that penicillins can actually refer to a whole class of antibiotics which all use β-Lactam and the specific set of antibiotics:

benzylpenicillin (penicillin G), procaine benzylpenicillin (procaine
penicillin), benzathine benzylpenicillin (benzathine penicillin), and
phenoxymethylpenicillin (penicillin V). (from wiki)

It should be noted that more correct way to address the whole class of antibiotics would be β-Lactam antibiotics, not penicillins, and that if you wanted to talk about more specifically penicillin derived compounds you would be discussing penams. For even further clarification, penicillin as drug most likely refers to benzylpenicillin, and for the rest of this answer I will use penicillin to refer to benzylpenicillin.

Thus we should think of penicillin as an early antibodic that work by preventing the dividing/genesis of cell walls and certain organelles via binding to penicillin binding proteins (PBPs).

Methicillin is also a β-Lactam antibiotic, and it's MOA is similar to penicillin. It was developed/discovered after penicillin and was seen a answer to Gram-positive bacteria that were breaking down penicillin via β-lactamase. Methicillian still works by binding to PBPs, but it escapes the bacteria's counter to penicillin.

This leads us to address how penicillin resistance and methicillin resistance commonly occur in staph. First, many staph strains and other bacteria use β-lactamases to breakdown antibiotics so they no longer can bind to PBP's (1). But methicillin is particularly suited by its side chains to not be degraded by β-lactamases. In their ground breaking work on the subject, Hartman and Tomasz identified that methicillin resistance was not in the acquisition of a β-lactamase, but in a mutation in PBP's that prevented methicillin binding (2). There they tested 4 strains of staph, two were methicillin resistant (MR), and two were methicillian susceptible (MS). You will note that all but 1 didn't have β-lactamase activity, and where more susceptible to penicillin than methicillin (ibid).

BUT this does not mean that MR strains are not also penicillin resistant, instead it shows that the resistance can be independent of each other. Therefore "A" is wrong because it tries to draw a correlation that is not there. In reality many MR strains are also β-lactamase positive.

This also address the problem with "B." While it is possible that a β-lactamase could bind to methicilin and lead to degradation of the antibiotic, the main mechanism of methicillin resistance is the mutation of PBPs (ibid, 3), in particular BPB2a (4, 5).

We are then left with the task of figuring out why "C" is the correct choice. Indeed "C" is the given reason for the failure of "A" and "B," but we can still go deeper into how and perhaps why BPB2a mutated.

For that I think it is best that we turn back to Chambers' review of the subject. Forgive my over quoting, but it's done so well there and the text is now open.

Methicillin resistance is associated with production of a novel PBP
that is not present in susceptible staphylococci. Resistant strains of
S. aureus produce an additional 78- kilodalton PBP (Fig. 1), termed
PBP2a or PBP2' (assumed to be identical for the purposes of this
review), that has a low binding affinity for beta-lactam antibiotics.

...

PBP2a is highly conserved. Limited proteolysis of PBP2a from unrelated
strains of S. aureus (123) and coagulasenegative staphylococci (31),
whether homogeneous or heterogeneous, generates remarkably similar
peptide fragments.

...

Presumably PBP2a can substitute for essential PBPs when these have
been saturated by drug and can perform the functions necessary for
cell wall assembly (22, 122).

...

In some strains, PBP2a is inducible by beta-lactam antibiotics and its
production differs according to growth conditions (34, 122, 125, 159).

Unfortunately, they didn't quite have the staphylococcal cassette chromosome mec (SCCmec) figured out at that point. The genetics is quite complex.

How does MRSA genetically accomplish resistance?

As we already established, the resistance comes from the production of an alternate PBP, PBP2a. SCCmec is interesting for several reasons. First of all, it's much larger than a plasmid, and contains information for several genes. That's why it's called cassette chromosome. Further it normally incorporates into the same part of the genome in staph, in an area know as OrfX (6). This means that even during horizontal transfer, that the cassette has to direct it's integration into the genome, which is exceedingly uncommon, or at least there are not many other know examples (7, 8). This cassette can be spread horizontally between staph, and even with other species (ibid, 9). Even if the integration site (integration site sequence, ISS) is slightly different, this specificity is carried out by cassette chromosome recombinases (ccr), wich are also on SCCmec (8). This is carried out by ccr-medated recombination of the target chromosome, and further details on the process are considered outside the scope of this question.

The actual gene that encodes PBP2a is called mecA. But as we mentioned above, PBO2a production can be induced and regulated. It is likely less favorable to produce it in the absence of antibodies, and after serial passage of bacteria in antibiotic free broth, you find that PBP2a expression can drop drastically. Therefore regulatory and other useful proteins encoded by SCCmec. When placed in a β-Lactamase environment, MecR1 causes a single transduction cascade to start transcription of mecA (10). Conversely, MecI provides a negative feedback loop to MecR1, and in the absence of β-Lactamase, will lead to the down regulation of mecA (ibid, 11). The actual action of MecR1 is to cleave MecI, thereby remove the suppression of mecA by MecI. I actually learned something new when reading the wiki on MRSA, but didn't do further research on the subject:

mecA is further controlled by two co-repressors, BlaI and BlaR1. blaI
and blaR1 are homologous to mecI and mecR1, respectively, and normally
function as regulators of blaZ, which is responsible for penicillin
resistance. The DNA sequences bound by MecI and BlaI are
identical; therefore, BlaI can also bind the mecA operator to
repress transcription of mecA.

This represents the general pattern of resistance of MRSA, but there is a rich diversity in the particulars of how each strain manages expression. Two of the main identifiers are how the mecA gene complex and ccr gene complex are configured (carriage). The other two identifiers are the ISS and whether or not the ISS is repeated in the target chromosome (and how many times it's repeated) (8). If we just consider the mecA and ccr carriage, then we get a great summary from IWG-SCC (ref 8):

The mec gene complex is composed of mecA, its regulatory genes, and
associated insertion sequences. The class A mec gene complex (class A
mec) is the prototype complex, which contains mecA, the complete mecR1
and mecI regulatory genes upstream of mecA, and the hypervariable
region (HVR) and insertion sequence IS431 downstream of mecA. The
class B mec gene complex is composed of mecA, a truncated mecR1
resulting from the insertion of IS1272 upstream of mecA, and HVR and
IS431 downstream of mecA. The class C mec gene complex contains mecA
and truncated mecR1 by the insertion of IS431 upstream of mecA and HVR
and IS431 downstream of mecA. There are two distinct class C mec gene
complexes; in the class C1 mec gene complex, the IS431 upstream of
mecA has the same orientation as the IS431 downstream of mecA (next to
HVR), while in the class C2 mec gene complex, the orientation of IS431
upstream of mecA is reversed. C1 and C2 are regarded as different mec
gene complexes since they have likely evolved independently. The class
D mec gene complex is composed of mecA and ΔmecR1 but does not carry
an insertion sequence downstream of ΔmecR1 (as determined by PCR
analysis).

And

ccr gene complex.The ccr gene complex is composed of the ccr gene(s)
and surrounding open reading frames (ORFs), several of which have
unknown functions. Currently, three phylogenetically distinct ccr
genes, ccrA, ccrB, and ccrC, have been identified in S. aureus with
DNA sequence similarities below 50% (Fig. 2 and 3). The ccrA and ccrB
genes that have been identified to date have been classified into four
allotypes. In general, ccr genes with nucleotide identities more than
85% are assigned to the same allotype, whereas ccr genes that belong
to different allotypes show nucleotide identities between 60% and 82%.
All ccrC variants identified to date have shown ≥87% similarity; thus,
there is only one ccrC allotype. We suggest describing their
differences as alleles by using previously used numbers, e.g., ccrC1
allele 2 or ccrC1 allele 8.

All of this is nicely summarized in their table:

\begin{array} {|r|r|r|}
\hline
SCCmec ~type &ccr ~gene ~complex &mec ~gene ~complex \\
\hline
I &1 ~(A1B1) &B \\
\hline
II &2 ~(A2B2)&A \\
\hline
III &2 ~(A3B3)&A \\
\hline
IV &2 ~(A2B2)&B \\
\hline
V &5 ~(C)&C2 \\
\hline
VI &4 ~(A4B4)&B \\
\hline
VII &5 ~(C)&C1 \\
\hline
VIII &4 ~(A4B4)&A \\
\hline
\end{array}

To sum up, methicillin-resistance is caused by the encoding of a novel PBP, PBP2a, along with other factors, which is both genetically stable and transferable via the use of SCCmec.

References:

(1) Pathak A et al. High prevalence of extended-spectrum β-lactamase-producing pathogens: results of a surveillance study in two hospitals in Ujjain, India. Infect Drug Resist. 2012;5:65-73. doi: 10.2147/IDR.S30043. Epub 2012 Apr 5. [Note that many of the great sentinel studies on drug resistant bacteria occur in the massive hospitals in India].

(2) B Hartman and A Tomasz. Altered penicillin-binding proteins in methicillin-resistant strains of Staphylococcus aureus. Antimicrob Agents Chemother. 1981 May; 19(5): 726–735.

(3) Liu, H. et al. Detection of borderline oxacillin-resistant Staphylococcus aureus and differentiation from methicillin-resistant strains. Eur J Clin Microbiol Infect Dis. 1990 Oct;9(10):717-24.

(4) Tawil N. et al. The differential detection of methicillin-resistant, methicillin-susceptible and borderline oxacillin-resistant Staphylococcus aureus by surface plasmon resonance. Biosens Bioelectron. 2013 Nov 15;49:334-40. doi: 10.1016/j.bios.2013.05.031. Epub 2013 Jun 4.

(5) Chambers HF. Methicillin-resistant staphylococci. Clin Microbiol Rev. 1988 Apr;1(2):173-86.

(6) Huletsky A et al. New real-time PCR assay for rapid detection of methicillin-resistant Staphylococcus aureus directly from specimens containing a mixture of staphylococci. J Clin Microbiol. 2004;42(5):1875-84. DOI: 10.1128/JCM.42.5.1875-1884.2004

(7) Schoenfelder SM et al. Success through diversity - how Staphylococcus epidermidis establishes as a nosocomial pathogen. Int J Med Microbiol. 2010 Aug;300(6):380-6. doi: 10.1016/j.ijmm.2010.04.011. Epub 2010 May 6.

(8) IWG-SCC. Classification of staphylococcal cassette chromosome mec (SCCmec): guidelines for reporting novel SCCmec elements. Antimicrob Agents Chemother. 2009 Dec;53(12):4961-7. doi: 10.1128/AAC.00579-09. Epub 2009 Aug 31.

(9) Stürenburg E. Rapid detection of methicillin-resistant Staphylococcus aureus directly from clinical samples: methods, effectiveness and cost considerations. Ger Med Sci. 2009 Jul 6;7:Doc06. doi: 10.3205/000065.

(10) Jensen SO and Lyon BR. "Genetics of antimicrobial resistance in Staphylococcus aureus". Future Microbiol 4 (5): 565–82. doi:10.2217/fmb.09.30. PMID 19492967

(11) Oliveira DC, de Lencastre H. Methicillin-resistance in Staphylococcus aureus is not affected by the overexpression in trans of the mecA gene repressor: a surprising observation. PLoS One. 2011;6(8):e23287. doi: 10.1371/journal.pone.0023287. Epub 2011 Aug 2.

nutrition - Which part of oranges contain fiber?

Cellulose is one of the most common sources of fiber in the nutritional sense. Because oranges are plants, their cells have cell walls, made out of cellulose, so some of the fiber in an orange is surrounding each individual cell. Both vascular cells and pith cells tend to have particularly thick cell walls, so they are probably higher in fiber (this article also suggests that the pith is particularly high in fiber - vascular tissue is probably not mentioned because it is less prominent).

diy biology - DIY extraction and long term storage of human DNA sample?

If you have access to a centrifuge, either spin columns or phenol:chloroform will give very pure, high-quality DNA. Even with dirty methods, you can re-extract the product several times, to sacrifice yield for purity. Just be very clean. Whatever method you use should remove salts and proteins, which are the major contaminants. I won't go too much into how to extract DNA, as that's a whole separate question - but the most important thing is that purer is better.

You should resuspend in Tris-EDTA. Tris buffer maintains pH at slightly acidic (best for DNA) and EDTA chelates metal ions which can catalyze oxidative damage of DNA. Very pure distilled water works too, but if you get contaminants they will do more damage.

Afterwards you can store the DNA for quite some time provided it's frozen. At -20C you can store DNA for years. It may not be perfect quality when you pull it out a decade later, but most of it will be good, and I'm sure it will be okay if you use a good sequencing method (and I'm sure sequencing technology will advance more in 10 years than the degradation of your DNA). The good news is that you can simply store it in your freezer, and it will be okay. -20C particularly is not hugely important, you can probably get away with -10C or so - the crucial thing is for it to be frozen, not liquid (this vastly reduces diffusion).

If you want to do it like a pro, you would put it under -80C. This is considered very safe for multiple years. You can do even better by precipitating it with ethanol, and then storing at -80C. In my opinion, this -80C is overkill - DNA is fine, for the most part, stored at -20C and even 4C, especially if you work reasonably clean and contamination-free. If you had some extremely valuable, very sensitive DNA, sure, do the -80. But just personal sequencing/genotyping? Just extract a bit extra DNA (a couple micrograms).

The really safe method is liquid nitrogen, which stops practically all chemical activity. Higher temperatures are too cold for most DNA-damaging reactions to proceed at a significant rate, but the molecules still move around. At -200C, they stop dead. But, once again, overkill unless you are saving very critical DNA for centuries later.

Source.

Three simple things I can recommend that are less obvious: First, do not handle your sample with hands, even gloved. Use some kind of plastic tweezers. Hands are warm and will locally warm up the sample. I would go as far as to put the sample tube in another box so that there is no direct contact. Second, avoid freeze/thawing. Whatever your storage system is, make sure it is very reliable. Third, wrap it in something opaque, to minimize light exposure.

Note as per Chris's comments: Always consult the MSDS of the substances you work with and take appropriate safety precautions! Always make sure to receive proper training before working with hazardous materials, and never purchase illegal contraband without appropriate authorization!

evolution - Genetically speaking, are dogs exactly similar to humans and chimps both?

Richard Dawkins mentions in his book The Greatest Show on Earth that dogs are exactly similar to both humans and chimps. Supposing that a cell contains the genetic similarity between 2 species, he says

The human/dog cell should have an identical resemblance score to the chimpanzee/dog cell because humans and chimpanzees have exactly the same degree of relation to dogs. It should be identical, too, to the monkey/dog cell and the lemur/dog cell. This is because humans, chimpanzees, monkeys and lemurs are all connected to the dog via their common ancestor, an early primate (which probably looked a bit like a lemur)

He later says that this will be found within "statistical margins of error".

Because the common ancestor of both chimps and humans was more similar to chimps than to humans, it stands to reason that chimps will be more genetically similar to the common ancestor than humans. Therefore (not a direct therefore), dogs and humans can't be exactly similar as dogs and chimpanzees are, even theoretically. Humans and apes are even more dissimilar. Therefore ape/dog cell will not be exactly same value as the human/dog cell.

Please explain where I am wrong.

biochemistry - What is/are the molecular differences between HDL and LDL cholesterol?

First of all, we should specify that there is no such thing as "HDL-cholesterols" and "LDL-cholesterols". On the same note there is no such thing as "good cholesterol" and "bad cholesterol": cholesterol is just one molecule, with this chemical structure

What blood tests generally report is HDL-C and LDL-C, that is the amount of cholesterol in HDL or LDL respectively (again, cholesterol is always the same molecule, whether in an HDL or in an LDL).

HDL (high density lipoprotein) and LDL (low density lipoprotein) are lipoproteins, aggregates of proteins and lipids that can carry, amongst other things cholesterol.
There are 5 major types of lipoproteins, called chylomicrons, VLDL, IDL, LDL, and HDL and are distinguished by their size, density and the proteins they are composed of.

The main function of lipoproteins is that of carrying lipids (=fats) around the organism in the blood. The problem is that lipids are not soluble in water (try to pour some oil in a glass of water) and blood is mainly composed of water. Lipoproteins, on the other hand, have a hydrophilic (="water-loving") exterior and a lipophilic (="fat-loving") interior, like this:

In the picture, the "balls" represent proteins, called apoproteins, and the C represent cholesterol and T tryglicerids, which are both lipids.
As you can see, all the fats are inside the lipoprotein, but the exterior, being soluble in water can be easily dissolved in the blood.

The biochemistry of lipoproteins is quite involved and I will not go into details here (but please leave a comment if you want further explanations) but, to simplify things:

• HDL bring lipids from the periphery back to the liver


• LDL bring lipids from the liver to the periphery

It is very important, at this point, to note that lipids are a physiologically important part of our organisms. All the cells in our body contain lipids: the membrane of each cell in the body is made up of lipids (called phospholipids) and also contain cholesterol. In fact, cholesterol is extremely important for the correct functioning of the body as, for instance, it is used as the base to make many hormones (the so-called steroid hormones, such as estrogen, progesterone, cortisol, testosterone etc).

However, too high levels of lipids, particularly cholesterol, are not beneficial, as high cholesterol levels have been in fact linked to many cardiovascular diseases, which we hear a lot about these days.

So, because HDL tend to remove the lipids from the circulation and bring them back to the liver they can be considered as some sort of "cleaners", that remove excess cholesterol from circulation.

biochemistry - Why do living organisms replicate itself or procreate

This is a very interesting question but the answer (or as much of the answer as is known) can fill a few books. There are many many signals that control cell division.

As a horrible simplification, the cell can be compared to a car parked on a slope with a driver's foot on the brake. If she lifts her foot, the car will roll downhill. In the cell, there are various proteins (P53 is the most famous) that have their metaphorical foot on the brake. Various external and internal stimuli can cause these proteins to stop suppressing replication and the cell will then continue its cycle and replicate.

So, a cell's "natural state" is to replicate, there is a complex network of interacting factors (primarily proteins) that actively block replication in resting cells. When the conditions are "right" (what that means depends on the cell in question) the block is removed and the cell replicates.

biochemistry - What biochemical molecule viewer allows for changes in amino acids and resulting tertiary structure?

If I understand what you're attempting to accomplish, as David said, this is a vigorous area of study in structural biology. I'll start by saying that a single amino acid substitution will often make virtually no difference in a structure, but there are proteins where a couple substitutions will convert an all alpha-helical protein to all beta-sheet, so I'll leave it to you to judge what's worth trying. There are three routes you can take:

First, for small changes, pymol does have a built in force field ("molecular sculpting") and residue mutagenisis. Chimera has a tool called "minimize structure" that are probably better developed. And VMD has the force field tool kit plugin.

If you expect larger changes, you might go with a full simulation package like NAMD or CHARMM. They would take significant effort to get running, but they're there.

Finally, you can just go with an empirical structure prediction server. All you do is open your sequence file, make your substituions there, upload it to the server, and wait for them to email you the results. They'll do sequence alignments to find relevant PDB files and everything. I recommend the Robetta server (running David Baker's Rosetta). http://robetta.bakerlab.org/

marine biology - Which poison makes seastars inedible to possible predators?

In the new citizen science project (see: Sea Floor Explorer), numbers of seastars, scallops, crustaceans and other animals are counted. Already one can see a heavy bias in favor of seastars, both the fat and brittle kind.

I would be interested in why this creature is so succesful, especially if it is poisonous to e.g., crustaceans, and what poisons exactly are responsible.

genetics - What is the biological mechanism underlying caffeine intolerance? (CYP1A2 or other?)

I have found that caffeine is mostly metabolized over CYP1A2 (as we know), but also over CYP1A1, CYP2E1 and CYP3A4. The question is how much the individual can cope with this alternate pathways if he is a CYP1A2 poor metabolizer. [1]

Secondly I found in my pharmaceutics textbook that CYP2A1 activity determination is indicated due to undesirable side effects to caffeine and theophyllin.[2]

UPDATE: 19.03.2013 12:30 GMT+1

@dd3: To clarify the second statement: I used the approach that theophyllin and caffeine are similar xanthin derivates. Since theophyllin is used as therapeutic drug in respiratory diseases (COPD etc.), I thought that scientific interest would be greater. And yes CYP1A2 plays an important role in both theophyllin tolerance and intollerance.

I found some new sources:

At first a study with CYP1A2 knock-out mice, which shows that the elimination of theophyllin takes 4-times longer in CYP1A2(-/-)mice. And they also assume that the same behaviour is also applicable to caffeine. [3]

Also there are two clinical studies by Japanese and Turkish scientists. The Japanese conclude, that theophyllin should be used with care in CYP1A2 poor metabolizer (even in haplotype poor metabolizer), since theophyllin has a narrow therapeutic range.[4] But the Turkish scientist assume that according to their findings, theophyllin is also metabolized over alternative pathways such as CYP2A13, CYP1A1, CYP2E1, CYP2D6 and CYP3A4. And according to this the genetic status of CYP1A2 is not as important as expected. [5]

Conclusion:
Assuming that theophyllin and caffeine are metabolized similarly, you can conclude that a mutation in CYP1A2 would lead to caffeine intolerance. In my experience people with caffeine intolerance describe severe nervousness after drinking a cup of coffee. Fatal cases I know were due to high consumption of energy drinks in children without or at least not known caffeine intolerance.

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Sources

Further Reading:

structural biology - What is a good list of unsolved protein structures?

There are some funded projects and analyses available just for this purpose.

Structural genomics or high throughput structure projects take all available peptide sequences group them into families and make sure sequence families pointing to most likely novel folds were available.

Here are the status and target list for the joint center for structural genomics. This list is filtered by species as well as by project status.

Their analysis is availble for us to browse through. http://www1.jcsg.org/prod/newscripts/psca/help/document.cgi

Sorry this isn't so thorough. Nature also hosts Target Track, which allows several high throughput structure centers to coordinate their efforts. Each might have resources which could do your work for you.

toxicology - copper vs aluminum, what's the safest for health?

Assuming the answer can't be C) Stainless Steel I would go with Aluminum.

The USDA specifically mandates (1) stainless steel 300:

"Milk contact surfaces shall be made of stainless steel of the 300
series, equally corrosion-resistant non-toxic metals or heat-resistant
glass."

Is the copper tinned? From what I can tell after reading some old sources (2) un-tinned copper will be corroded by milk. You have the advantage of a cool temperature lowering contamination risk (3), but many states following the FDA specifically removed the allowance of tinned copper (Sec. 22-201).

While the effects of life long dosing of Al are becoming more and more clearly tied to Alzheimer's (4), the effects build up over time. Copper has a tendency to be more acute (5) and pronounced (6, 7), and further it can tasted in low amounts and discolor the food (8). It can be said that water flows through Cu pipes, but soda is put in Al cans.

The research for this has been quite enjoyable, and led to things I didn't even think of. A alternative cleaning site has even recommended using milk to clean Cu pans.

Again so my final recommendation is to follow USDA guidelines and use stainless steel, but my second choice would be Aluminum.

Citations:

(1) USDA. 2011, July. Milk for Manufacturing Purposes and its Production and Processing.

(2) US DOC. 1917, April. STRUCTURE OF THE COATING ON TINNED SHEET COPPER IN RELATION TO A SPECIFIC CASE OF CORROSION. Technologic Papers OF THE Bureau of Standards.

(3) COMMITTEE ON COPPER IN DRINKING WATER, NATIONAL RESEARCH COUNCIL. Copper in Drinking Water. NATIONAL ACADEMY PRESS. 2000.

(4) Walton, J.R. Aluminum Involvement in the Progression of Alzheimer's Disease. Journal of Alzheimer’s Disease 35 (2013) 7–43. DOI 10.3233/JAD-121909

(5) Reilly C. The dietary significance of adventitious iron, zinc, copper and lead in domestically prepared food. Food Addit Contam. 1985 Jul-Sep;2(3):209-15.

(6) Conor Reilly. Metal Contamination of Food:
Its Significance for Food Quality and Human Health. Pg 50. John Wiley & Sons, Apr 15, 2008

(8) ibid pg. 16

(7) Lee A. Price, et al. Chronic copper toxicosis presenting as liver failure in an Australian child. Pathology. 1996, Vol. 28, No. 4 , Pages 316-320 (doi:10.1080/00313029600169264)

genetics - How do mutations come to be shared by all cells?

It's my understanding that various hazards can damage the DNA in our cells, causing mutations.

But whenever I picture this, I see the damage being done to one of our tissues (for example, our lungs due to smoking, or our skin due to UV rays).

When I think about this, I see that... many cells in a smoker's lungs, or many cells on the back of a beach-goer's neck, may have mutations in their DNA. But only the cells in that tissue have these mutations... the other cells in our body would not have the same mutations.

In particular, sperm and egg cells would not have the same mutations, so the mutations due to smoking and UV rays shouldn't pass on to children.

Are there instances where mutations that occur over the course of our life are spread to every cell, including sperm and egg cells, so that every cell reflects the mutation, and the mutation is passed onto our offspring?

evolution - Won't natural selection miss the overall minimum of a function?

What I think the question is "Why wouldn't an organism be more efficient from selection than the environment demands?" Please let me know if I'm hitting the mark here.

A scenario suggested by the question is this: If there is selection pressure on say an animal to resist a disease, and then it evolves two resistance systems to the disease. This could be an immune response and a taste for a certain plant containing compounds with remedial properties. If either system is adequate to resist the disease, hasn't selection gone above and beyond what is needed?

If so, the answer is either not recently, or all the time.

First, for 'not really' you have to consider the importance of competition. Reading about the Red Queen's Hypothesis is helpful here.. First there is a natural random mutation rate, which can cause one of the system to become less effective. Or if the disease is also changing to increase its efficiency, then either one or both of the defense mechanisms in this case would fail from time to time. Then having two systems would not be too much. There is a clear benefit to having redundant systems of resistance here. For both these broad categories of reasons, you have much redundancy and interdependence among the genes which create traits in living things (phenotypes). Because of the background mutation rate, traits which are not needed disappear relatively quickly; because of competition, those which convey an advantage, even if a small one, have a strong likelihood to stay in the gene pool.

now: "all the time" There are cases where traits are exhibited that are not efficient though. Evolution works over generations, typically selection influences traits on the order of 10s of generations and the population can show traits which are not helpful if the environment or the competition has changed drastically.

An example of this is the current obesity epidemic in the developing world. The sudden availability of cheap food has caused those people who have access to become obese. This is because they have a heavily reinforced trait to save up fat because humans experience famines regularly. Its going to take a long time before efficient energy storage in human beings is lost. In the meantime, people are not living to reproducing age at the same level of fitness they might have.

I want to add a note on genetic algorithms. The difference between genetic algorithms to achieve the same efficiencies as biological systems are worth thinking about:

• As far as failing to find a global minimum, natural selection usually has many more samples. A typical selection experiment with flies or worms often have thousands or tens of thousands of individuals screened. GA models of reasonable complexity have usually a few score at most - am I right? A bacterial or yeast experiment can have 10^9 individuals.

  
  
  

  • The genetic system of the chromosome itself is tremendously complex. We can't even model itself and so the product of millions of generations of selection already will has a heretofore unmodelable response to selection.

  
  

  • The typical selection environment is equally undefinable, so a survey of living things in a complex environment has unpredictable effects. While most of us think as laboratory experiments as being less complex, its not completely true. I was at a talk recently that mentioned how E coli K12 seems to have diverged in various laboratory environments despite the fact that its mostly been in frozen stocks since being isolated in the mid 20th century.

  
  

neuroscience - Why do neurons have a negative resting potential?

Neurons expend the majority of their energy powering ion pumps to maintain the chemical gradients that power their electrical activity. To have a negative resting potential, neurons leak potassium across the membrane, which seems like a terrible waste of energy to me. I would like to know what benefit a neuron receives in exchange for this seemingly unnecessary metabolic load.

I am not asking how the resting potential is achieved. I am also not interested in the trivial answer: that the voltage-gated channels are configured to require a transition across the -40mV or so threshold in order to fire an action potential. It seems to me that this threshold is arbitrary; if there was no advantage to maintaining this gradient then neurons would have evolved to avoid it.

Any ideas? Or better yet, pointers to places where this has already been answered?

My best guess so far looks like this: The total range of available voltages is more-or-less fixed from -90 to +50mV. We want to avoid getting too close to either end, since the channels become less effective near their reversal potentials, so maybe the effective range is more like -70 to +30 (to go outside that range, we must sacrifice speed). Within that 100mV range, we leave the bottom 30mV or so for EPSP integration, and the other 60mV for action potentials. Now, if the resting potential was 0mV, the available dynamic range for integration and spiking would be much smaller which probably translates to making the output noisier.

behaviour - Why do dogs try to cover their poop?

It may seem obvious to us humans to hide our excreta, but this is not quite normal behavior for animals.

Interestingly, dogs have the habit to pee all over the place. It's know that they do so to mark their territory. So when they want to mark their territory, why do they cover up their poop?

I found an old web article where someone asks the same question, without getting a credible answer. He quotes a Yahoo Answers answer making the following claim:

This behavior is natural in dogs. They cover up their "waste" so that
an enemy does not find them, from the scent of the poop or pee. It is
an instinct handed down from wolves, who hid their scent by covering
up their feces in leaves, sticks, soil, or other nearby natural
materials. They also rolled in animal carcasses to hide the scent of
them. Your dog is just using her natural instinct to protect herself
from predators.

Another things that dogs do, called marking, is when the dog pees in a
certain area. They do not cover it up, as it is marking a territory as
their own. Male dogs usually do this on trees, wooden posts,
furniture, and other things. Female dogs do this in heat. Dogs do not
poop to mark something, only pee. When you dog pees or poops and then
covers it up, this does not mean she is marking her territory. Just
wanted to add it so you don't get confused. :)

I find it hard to believe these to opposite claims. One time dogs want to mark their territory and the other time it's scared from predators. I know many dogs that do not cover their pee, but do cover their poop, sometimes even within the same walk (and so the same territory).

If this is true, why do dogs do both in the same walk?

On Wiki Answers I found this answer:

The animals are not actually covering up the pee or pooh but spreading
their scent. This often happens with animals that are dominant (for
instance show dogs).

It's so that dogs never actually cover their poop anymore, they only perform some random scratches, throwing a little sand on the turd, sometimes even nothing. That fact makes this answer quite more likely than the previous one.

Another take that's similar to the previous one is this one from Dogster:

So, why do dogs scratch with their hind legs after defecating? You
might think the dog is trying to cover up his poop like a cat does,
but it’s actually a way to mark territory, with the scratch marks in
the ground pointing to the scent the dog has left.

I also found an eHow article on this subject. It seems to agree with the previous two explanations, but is more detailed.

It is normal for dogs of both sexes to vigorously kick the ground with
their hind legs after defecating. This is called scraping or peeling
out. Some dogs will also do it after urinating. Dogs are descended
from wolves, which also perform this behavior. It is not a bad habit,
but a vital part of a dog leaving a visual message and scent message
to any other dogs that happen to pass by.

They also say that the specific reason why they spread scent with their paws is because paws just contain a lot of scent.

Dog paws contain scent glands. There are also glands in between the
toes. The action of scraping the paws against the ground helps release
the scent inside of the glands. Dogs scrape the ground in order to
increase their scent on the area near the feces pile, according to
veterinarian Dr. Justine Lee. Before domestication, dogs wandered in
large territories. One vital way to communicate with other wandering
dogs is through scent marking. This instinct has not been bred out of
the domestic dog.

So, which theory is the most valid? I tent to go for the scent one. Any additions?

bioinformatics - Determining if a Protein Model Contains a Backbone Clash

The way to check for steric clashing between any two atoms, backbone or otherwise, is to compute their Euclidean distance. If a and b represent two atoms (with a_x being the X coordinate of atom a and so forth), you can calculate their Euclidean distance as follows.

d(a, b) = sqrt( (a_x - b_x)^2 + (a_y - b_y)^2 + (a_z - b_z)^2) )

So essentially the idea would be to calculate the pairwise distance between each of the backbone atoms. For any pair of atoms, there is steric clashing if the distance between them falls below a certain threshold. If I remember correctly, this threshold is the sum of the van der Waals radii of the two atoms.

genetics - Bicoid regulation of hunchback

I'm learning about development via the example of Drosophila embryogenesis. I understand that bicoid regulates hunchback, among other genes. My question whether the regulation is direct or indirect? In other words, does the level of bicoid directly govern the expression of hunchback, or are there steps in between?

cloning - Deletion errors with Phusion Polymerase?

In my own personal lab experience, I got some unexpected results using Phusion polymerase. However, I have not seen deletions, only insertions (ranging from single bases to 3 tandem copies of a primer sequence). This is not an answer to your deletion question, but it does suggest unusual things might happen.

I have seen deletions with T4 DNA polymerase during "blunting" reactions. According to the NEB website:

Q10: Is T4 DNA Polymerase active at room temperature?

A10: We suggest 12°C. The DNA ends "breathe" at higher temperatures allowing the exonuclease to remove nucleotides past blunt.