Why does one combine PCR and cloning as ways for amplification of sequences? Why does one combine PCR and cloning as ways for amplification of sequences? Don't they produce the same result? I was reading the paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1864885/ and got confused by the following passage:

  Cloning and Bisulfite Genomic Sequencing

  Each bisulfite-converted DNA
  sample was subjected to PCR by primers that did not discriminate
  between methylated and unmethylated sequences, using a GeneAmp PCR
  core reagent kit (Applied Biosystems). The primer sequences are listed
  in Table 1, and reaction conditions are listed in Supplemental Tables
  1C and 1D (available online at http://ajp.amjpathol.org). Each
  subsequent PCR product was TA-cloned into pGEM-Teasy vector25
  (Promega) for transformation into Escherichia coli strain JM109,
  according to the manufacturer’s instructions. Clones were picked
  randomly and colony PCR was then performed using vector primers T7 and
  SP6 to amplify the cloned inserts. Cycle sequencing was performed
  using BigDye version 1.1 (Applied Biosystems) and an automated
  capillary DNA sequencer Genetic Analyzer 3100 (Applied Biosystems).
  The sequences obtained were aligned and compared using SeqScape
  software (Applied Biosystems). The completeness of bisulfite
  conversion was first confirmed before scoring. The CpG sites sequenced
  as cytosine or thymine residues were scored as methylated or
  unmethylated, respectively. The methylated site frequency was
  calculated for each sample by dividing the total number of methylated
  sites over all cloned CpG sites.

Can someone comment on what purpose the cloning serves when the amplification is already done by PCR?

There are several reasons to clone a PCR product but the main reasons include expressing the product and maintaining the library inexpensively.

In the study you mentioned, the cloning and transformation is apparently done for obtaining single clones (from single colonies).

  Clones were picked randomly and colony PCR was then performed using
  vector primers T7 and SP6 to amplify the cloned inserts. Cycle
  sequencing was performed using BigDye version 1.1 (Applied Biosystems)
  and an automated capillary DNA sequencer Genetic Analyzer 3100
  (Applied Biosystems).

Since the original PCR would have a mix of different sequences, cloning is done to separate them out for the ease of studying them by sequencing. If they don't separate the sequences, they would have to use NGS (or more expensive methods like PacBio for longer reads). They have used Sanger sequencing. This article was published in 2007. At that time NGS was not as cheap as it is today and was hence not used by everyone. Also, the NGS machines of that time had even smaller read lengths (~40 for Solexa/Illumina GA and ~75 for GA-II). Considering these, Sanger sequencing may have been preferable to the authors of this paper. However, as I mentioned before, Sanger's method cannot be used for sequencing pooled samples; you need pure templates or else there will be mixed signals and base calling would be inaccurate.

(See the example chromatogram below: look at the position with the Y which has mixed T and C signals. It is not from a pooled sample, though).

Therefore cloning, transformation and colony picking was necessary.

Moreover, in many cases picking individual clones would be necessary for performing functional assays to associate phenotype with genotype.


Do ants really find the shortest path to a food source? There exist many computational intelligence algorithms based on the observation that ants deposit pheromones in such a way that they find the shortest path to food sources. This logic is used to optimize computer networks.

I cant really relate to that. I have seen ants take an extremely long path to food. This is not always for safety reasons either. What do biologists have to say about this?

Short answer

  Do ants really find the shortest path to a food source?

No! But they can find a decent path

Longer answer

Optimization algorithms are used to search through a possibility space that is too large to explore every single possibility. Such algorithms attempt to find a good enough solution, often without necessarily knowing how 'good' the found solution is to the best possible solution. So optimization algorithms don't always find the best solution. Actually, most of the time, they do not find the best path but a good enough one in a reasonable amount of time.

Same holds true for ants. In the analogy, an ant colony is an agent based algorithm where agents leave pheromone trails. The concentration of the pheromone depends upon the length of the trail. By following the trails that smells the strongest and by regularly making small errors (so that they can keep exploring other paths), they end up with a decent solution. For more info, just google How do ants find their path?.


What could the etymology of Phallodriline be? I'm reading about a series of gutless worms described in several papers as phallodrilines. A search in the World Register of Marine Species shows that there is a subfamily called "Phallodrilinae", but then, in at least one paper this term is used to collectively describe gutless worms in several taxa including Oligochaeta, Annelida, and Clitellata. Since they're also described as club-headed I'm assuming that "Phallo-" is from the Latin for penis, but what would be the rest?

-o- linking vowel indicates Greek. -i- is Latin, unless the second word starts with a vowel (many -ectomy words for example). This is irrespective of declension or gender. Weird I know.

In fact, Latin phallus is from φαλλός.

The second part is worm δρῖλος (drilos). Actually it can also mean penis, but let's gloss over that...


How are the physiological properties of mitochondria measured? this is my first question on BiologySE. I am a Physics and Mathematics student currently doing a project on cell growth simulation. I am doing literature survey and I have a question about cellular biology experimental methods.

I understand that the membrane potential is a measure of mitochondrial functionality (higher potential means more efficient electron transport chain). Additionally, the mitochondrial volume is also an indicator of mitochondrial efficiency (higher volume, higher area, more places to do electron transport).

I would like to have some points elucidated.

In particular, can these mitochondrial membrane potential and volume...

be measured for a single cell, or only in a population?
be measured non-destructively, leaving the cell alive?
be measured simultaneously, or experiments measuring one necessarily make the other unavailable?

I am thinking mostly of in vitro experiments of course.

A simple method would me to express a fluorescent protein in the cell that specifically localizes to mitochondria. mito-dsRed is a Red Fluorescent Protein which has that property; it can be expressed from a plasmid.

Using fluorescent microscopy and image analysis, you would be able to measure the geometric properties of the mitochondria. This can be done at a single cell level too (using confocal microscope) and non-destructively. Volume can be measured by what is known as Z-stacking— an automated technique by which the microscope takes several 2D snaps at different planes and stacks them to construct a 3D image.

You can implement this in live cells too; this method is called live cell imaging.


Compatibility drugs info Let's suppose that I take a DrugA for ProblemA and then I got this ProblemB and started to take DrugB. Are there general rules I can look up to figure out whether I can take DrugA & DrugB simultaneously?

I mean drugs can cancel each other or vice versa increase effects of each other (in an extreme extend); or one of drugs has adverse effects that are bad for the other drug.

I would like to start by suggesting you talk to whoever prescribed you the drug or your pharmacist. They should be most up to date with interactions and there are some interactions which may only affect you more seriously because of your medical history or current conditions.

Here are some sites that you can check drug interactions in order of popularity:

Medscape

Drugs.com

Healthline

WebMD

RxList


How hard it is to determine a 3d structure of a protein? I seeing tens of thousands of PDB files on the internet. I really want to determine a 3D structure of my protein of interest. I've heard that 3D structure determination is a complex, expensive, and specialized procedure that can take months or years and is hard to perform routinely or even purchase commercially.

Could you please explain why and how hard it is? What are the requirements and how big of a budget is typically needed to perform this kind of experiment?

Experimental protein structure determination is hard: the most common method is X-ray crystallography, which can be done in a few months if you are lucky and can take years if you're not. The problem with X-ray crystallography is that you need good protein crystals, and in most cases, proteins don't crystallize very well, so it takes a lot of time (and a lot of purified protein) to get the right crystal. (In the comments section Cody added some good links with more in-depth abut X-ray crystallography for structure determination relating to ATP synthase).

The cost is mainly based on the materials & manpower you need for this, and you need to test a lot of different solutions to crystallize your protein in, which aren't very cheap. If you don't have access to specialised equipment for making the crystals (mostly pipetting robots) or the measurement (X-ray beamline), this is going to be super expensive.

Crystallography requires protein crystals, which are sometimes too troublesome to obtain. Other methods that do not require crystals, such as NMR and cryoEM, are even more difficult to perform though less luck dependent. These techniques rely on very expensive equipment and often cannot resolve the structure as precisely as protein crystallography. So unless you can find one of the few people who have experience with these methods, you'll run into a lot of additional problems.

There is also computational structure prediction, which only needs a powerful computer. However, unless your protein is very similar to one with a known structure it will probably not work reliably. As mentioned in the comments there are web server's for the established methods and progress is constantly made on new(er) algorithms, so depending on your needs it's definitely worth a shot to try computational structure prediction.


Entropy during neuronal signaling to begin with: I have some background in cognitive neuroscience, but have not intensely studied the biochemical background of neuronal signalling, so please correct me if my basic understanding is wrong.

As studying the generation of action potentials and EPSP/IPSP at synapses, I noticed that as those processes make use of the gradients, the actual signalling process works by resolving these gradients (i.e. the molecules flow without having a constant energy supply pushing them to do so). The big part of energy consumption during neural signalling is then actually needed for restoration of these gradients, transmitter reuptakes etc.

So if the above is correct, does that mean that the information "flow" in the brain is done by increase of entropy (which I intuitively understand as a increase of "unorderedness", but im not a physicist either...)? I have been told that biological systems actually want to resist the "natural" direction of entropy in that they want to keep themselves "ordered" to survive. I would have hence found it more intuitive if signalling would be acquired by an active decrease in entropy (followed by some sort of "passive" restoration). Is there any reason why that is not so? Are there other examples of signalling where that is the other way round?

Or am I just lacking understanding and messing up definitions?

Thanks for your help

In my view, thinking of entropy as something biological life has "wants" about is a bit mistaken. In general, entropy arguments regarding biology run into a major problem in that the interesting physical laws involving entropy required closed systems, and no biological system is closed, so it's a bit moot.

It makes more sense to think about what benefits "fighting against entropy" gives a biological organism, and I also think it makes more sense to think in terms of potential energy rather than entropy (even though they are of course related).

Neuronal signaling is best when it's rapid. By pumping ions against their gradient ahead of time, neurons establish a concentration gradient (which you can view as a decrease in entropy). This is indeed the active part. This also stores energy in the gradient, in that if a 'gate' were opened, the gradient would tend to equilibrate. Because the ions involved are charged, additional sensors in the membrane can respond to this changing electrical gradient.

  I would have hence found it more intuitive if signalling would be acquired by an active decrease in entropy (followed by some sort of "passive" restoration)

I think you might be mixing up the "action" verbs here. Think about pushing a rock up a cliff or lighting a firework. If you want that rock to be a signal, it's going to be a much more dramatic signal falling down the cliff than it was pushing it up the cliff. It's going to be much more dramatic lighting off the firework rather than extracting the needed ingredients from various places and assembling them. Processes that release stored energy tend to be a lot more dramatic and "active" despite being "passive" in terms of needing to add energy (besides activation).


Why does a frog's oxygen intake through the skin and lungs vary throughout the year? Why does a frogs oxygen intake through the skin and lungs vary throughout the year?  And why does the intake through the skin vary slightly while through the lungs dramatically? (Blue line = oxygen intake through lungs and orange line = through skin.) Thanks.

Cutaneous respiration is based, as every type of respiration, on diffusion of gases from a higher concentration (in water or air) to a lower one (in capillaries).

Citing from Johnson, Peter H. Raven, George B. (2002). "Respiration". Biology (6th ed.). Boston: McGraw-Hill. pp. 1053–1070:

In general, the rate of diffusion between two regions is governed by a relationship known as Fick’s Law of Diffusion:

R = D - A x ∆p/d

In this equation,

R = the rate of diffusion; the amount of oxygen or carbon dioxide diffusing per unit of time;
D = the diffusion constant;
A = the area over which diffusion takes place;
∆p = the difference in concentration (for gases, the difference in their partial pressures) between the interior of the organism and the external environment; and
d = the distance across which diffusion takes place.

As you can see, the rate of diffusion R can be increased:

By increasing A, the diffusion area;
By increasing ∆p, the difference in concentration;
By decreasing d, the diffusion distance.

In cutaneous respiration, nr.2 is not really an option; yes, capillaries can be optimised to bring blood rich in carbon dioxide and poor in oxygen really close to skin surface (which brings us to nr.3), but it's a lot less efficient than, for instance, lungs that can exhale air filled with carbon dioxide and replace it with fresh air. While the intake of oxygen of the skin remains more or less the same even with different metabolic demand, lungs can quickly adjust the breathing rate depending on the metabolic demand of the moment.

So, the answer to the question

  why does the intake through the skin vary slightly while through the lungs dramatically?

is that skin cannot regulate its gas exchange rate, while lungs can. This brings us to your first question:

  Why does a frogs oxygen intake through the skin and lungs vary throughout the year?

The answer lies in the biological cycle of the frog throughout the year: during cold months, frogs hibernate. In winter, frogs slow dramatically their metabolism and they don't need so much oxygen; thus, in this season they are able to rely only on cutaneous respiration. In other seasons they are active, and they have to breathe actively through their lungs to supply their blood with the necessary quantity of oxygen.


When is a DNA sequence a gene? I am a newbie is DNA sequencing and BioInformatics. I am writing a school project that determines whether a DNA sequence is a gene or not using a Machine Learning Algorithm, Hidden Markov Model. After understanding the the algorithm, I now want to know when we can say this particular DNA sequence is a gene. Any help or pointers would be appreciated. Thanks

We can devide algorithms for protein-coding genes in eukaryotes in two main categories:

Extrinsic, these algorithms rely on the comparison with external data sources,  such as comparing genomes
Intrinsic, I suggest you are more interested in this one when you acctualy want to predict gene coding regions on your own (If I'm wrong I will further explain extrinsic methods). The intristic methods are based on ab into predictions.

I will continue on Intrinsic methods, so what can we use to identify coding genes in the sequence. Ofcourse we need to know the charasticts of those coding regions:

Most of the time we see CpG Islands(regions of a higher than expected occurrence of CpG dinucleotides over a patricular region).

  About 70% of human promoters have a high CpG content (Wiki)

Those CpG islands are important for the regulation of gene expresion.

the basics of a coding sequence are the promotor, introns and exons.
you are probably familiar with the fact that a mRNA has to be spliced in order to cut the introns (non coding regions) out, this is done by the splicesome wich recognizes special sites where it can cut, So you can search for these sites in your DNA sequence.  I will summarize some points about the coding regions here:

CpG Island near the promotor
splice sites for splicesomes
Start and stop codons (I hope you are familiar with these)

There are more things to consider but I would to suggest to look at the algorithms of these programs: GENSCAN, FgeneSH, GeneMark, Xpound and to read this atricle which is about identifying the protein-coding regions


Formation of ammonia from air and moisture On extended bicycle trips I sometimes slept under a plastic sheet, which helped with mosquitoes on hot nights. But there was a noticeable build-up of ammonia which made this almost impossible for more than an hour or so at a time.

Air is mostly nitrogen $(N_2)$ and there is always water (containing hydrogen) on a humid day. But I wonder about the mechanism for the formation of ammonia under these circumstances? There are (according to Wiki) trace amounts of methane and $H_2$ in the air. But methane and hydrogen (g) are I think pretty stable.

I wonder if the presence of exhaled air (containing $CO_2)$ could be a factor?

Thanks for any ideas.

If you're absolutely sure it's Ammonia ($NH_3$) you're smelling, it's probably from you.

Ammonia will not spontaneously form at any significant rate from the air. Molecular Nitrogen ($N_2$) is extremely stable.

What can happen is that during marathon-type activities, muscles turn from carbohydrates (which are later converted into glucose and enter into the Krebs Cycle) as an energy source to proteins themselves.

One of the waste products of protein catabolism is Ammonia, which is excreted in your sweat if the body can't convert it into Urea ($CH_4N_2O$) quickly enough:

  Ammonia forms with the oxidation of amino groups (-NH2), which are removed from the proteins when they convert into carbohydrates. It is a very toxic substance and only one nitrogen atom is removed with it. A lot of water is needed for the ammonia excretion.


Microsatellite shifts (peak calling) GeneMapper! Thesis help! I'm a masters student attempting to conduct a parentage analysis on a population of fish for my thesis. My advisor and post-docs haven't been very helpful, so I need some help! I have dinucleotide microsatellite markers that I've run on a set of individuals.

I'm using GeneMapper 4.0 to score the alleles of said markers but something isn't making sense. My alleles are shifted to where they are not evenly distributed in their sizes. For example, at a given locus for one individual I have one allele peak at 152 while the other allele peak is at 161 (It's an obvious heterozygote).

This "shift" doesn't make sense considering my markers are dinucleotide and should be spaced 2 bp apart, right? So either 152 is actually 151/153 or 161 is actually 162/160. How can I score these and resolve this issue while keeping consistency for my analysis later? I see this shift everywhere and I've already ruled out contamination and I'm positive these peaks are real. Any pop gen people out there that have a clue what to do?

I've been stuck on this for weeks, no amount of web searching/paper reading helped.
Thanks!

Your markers are probably fine, especially because you keep seeing the same allele in multiple individuals. Dinucleotide repeats do not always copy perfectly. More likely, remember that the primers you use to amplify your microsatellites bind outside of the actual repeat region. You could have an insertion/deletion in the region between the primers and the repeat region, changing your allele sizes from to even to odd (or vice versa).


Origin of the biochemical term, Pi (inorganic phosphate) I would like to know when the term Pi (inorganic phosphate) was introduced in the representation of biochemical reactions, how it was originally defined, and the justification given then for using it rather than an individual species of phosphate.

(I would also be interested in the current justification, but that’s probably another question.)

Let me provide some background to my question. Phosphoric acid (H3PO4) has three ionizations, which produce successively the species: dihydrogen phosphate (H2PO4–), monohydrogen phosphate (HPO42–) and orthophosphate (PO43–). At pH 7.4, according to the Wikipedia entry on phosphate, the main species are the mono- and di-hydrogen phosphates (61% and 39% respectively). The term Pi must have been introduced in the 1950s at latest (perhaps before the war), at a time when there would have been little knowledge of the nature of the species involved in reactions involving phosphate — certainly not at the active sites of enzymes.

One of the reasons I am curious to know how the term was introduced is the extent to which it persists in 21st century biochemical text books, where it would seem that many authors either do not know or do not care to explain to their readers why they are still using it at a time when much more is known about the reaction mechanisms. Neither of two well-known texts explain the different ionizations of phosphate, and give only parenthetical definitions in terms of a single species — different in each case: Berg et al. referred to Pi as orthophosphate, whereas Nelson and Cox’s, Lehninger  Principles of Biochemistry referred to it as HPO42–.

Acknowledgement: This question was provoked by the SE-Biology question — Where is the H+ ion in this step of glycolysis coming from?

This terminology is at least as old as September 1944 when Enzymatic Synthesis of Acetyl Phosphate Journal of Biological Chemistry
155,  55-70 was published by Lipmann, which says:

Inorganic phosphate, referred to as Pi, was estimated
colorimetrically

See also the definition of "inorganic phosphate" and "orthophosphate" from this 1943 University of Wisconsin Thesis:

Compound:  Inorganic phosphate or orthophosphate
Definition: Phosphate whose calcium salt is insoluble in water-alcohol mixtures under the conditions to be described. E.G. NaH2PO4

In other words, "orthophosphate" was a generic term for mono, di, or tri basic phosphate.  It did not have the narrower meaning attributed in the OP.


Binomial nomenclature: Why am I seeing different genera with the same species name? I have looked online but still do not understand how two organisms can have the the same species names but be in different genera?

Do all genera share common species names?

Also which would be more closely related, two organisms with the same genus name but different species name or two organisms with different genus names but the same species name?

According to a textbook, the two with the same genus are more closely related, but I do not understand why?

Two different species can have the same species epithet if they belong to different genera ('species name' is referring to the full binomial name). Consider for example Pinus glabra and Ilex glabra

P. glabra

I. glabra

Two species can be have the same genus name (meaning they belong to the same genus) and will therefore necessarily have different species epithets (otherwise we would name them exactly the same way which would be very confusing). Consider for example Pinus glabra (again) and Pinus resionosa

P.glabra

P. resinosa

As a consequence, if two species share the same species epithet then it tells you nothing about how closely related they are. If they share the same genus name, then they belong to the same genus (except exceptions probably!).

For the above examples, the term glabra comes from "glaber" (latin) which means "Hairless". So the only thing you can tell from P. glabra and I. glabra is that they are probably both hairless when you compare them with their respective closely related species.


How do major and minor grooves arise in the DNA helix? I understand that they arise due to the pairing of bases of two opposite stands and are sites through which important proteins needed for replication and transcription of DNA interact. But I don't get how the arrangement of bases really generate the grooves.

First the MAJOR groove. This can be considered by forgetting that the two DNA strands are separate and thinking of them as merged together like a rope or an electric cable in my diagram below. The cable is wrapped around an axis, which can be thought of as an imaginary rod. One could wrap the cable tightly round the axis so it was always in contact with itself and no space in between (as on the extreme left), or one can wrap it round less tightly with space in between (subsequent images). The latter is what happens and the space left by the wrapping of the rope is the major groove (because it's wider than the minor groove we come to next).

So to your question, what causes this winding to be the way it is — which is to say what causes the particular pitch of the DNA helix? This is presumably the most thermodynamically stable conformation, maximizing the strength of the hydrogen bonding between the bases (most linear, not too close or too distant) and minimizes steric and electric replusion (the phosphate backbone is negatively charged).

Next the MINOR groove. We now have to consider that our 'cable' is actually two strands of DNA — a sugar phosphate backbone with the paired bases in the centre. Although the bases are in the centre, the space between the two sugar-phosphate strands is not completely occupied. This creates another groove - the minor groove - less wide and of quite different origin to the major groove, but still able to accomodate certain small proteins. As it happens, this is the case with the electric cable analogy illustrated. The cable is two electric wires, but they are encased in the same plastic inuslator.

So to your question, what causes the minor groove? This is just the three dimensional shape of the DNA double-strand which reflects the molecules that make it up. The large phosphate groups can be considered like wide tubes at either side, whereas the bases between the strands are flat and so lead to a groove, irrespective of whether it is wound into a helix or (in one's imagination) stretched out.

(The 'major' groove is exaggerated in size compared to the 'minor' groove in the cable analogy, but I hope it illustrates the difference between the two.)


Do vitamins help our memory? It is commonly believed that vitamins can help our memory.

Is this really true? What is the biological basis of this?

Is there any specific research paper on the subject?

There seems to be no effect of vitamins. This paper ("Preventing cognitive decline in healthy older adults." found no evidence for herbal supplements, vitamins or fatty acids improve cognitive functions.

There seems to be some evidence ("Preventing Alzheimer's disease-related gray matter atrophy by B-vitamin treatment.") that a cocktail of hig dosed vitamins including folic acid, Vitamin B6 and Vitamin B12 can slow Alzheimer's disease. But: The benefits were only seen in participants which had high blood levels of homocysteine. This amino acid is linked to a higher risk of heart disease for which the B vitamins are postive for the outcome. So this might only be helpful for people with too high homocysteine levels.

And its questionable if high doses of antioxidants (like vitamin A or E) are not only not helpful, but can cause actual damage. This is due to the fact that they catch up reactive oxygen species, which might otherwise trigger the cell to go into apoptosis and prevent it from becoming a cancer cell. Here is the paper: "Antioxidants accelerate lung cancer progression in mice.".


What is a catalytic domain of an enzyme? Is this another name for the active site of an enzyme? What does the structure of the catalytic domain of an enzyme look like?

Both parts overlap. Proteins are a chain of linked amino acids. This chain can be grouped into functional units which are called protein domains. Usually all parts of a domain are closely located in the protein and they form functional domains in the 3D structure of the protein. Proteins usually contain more than one domain (these are manifold but for example can be dimerization, activation or binding domains).

The catalytic domain is the part of the protein chain which contains the region where the catalyzed chemical reaction takes place. The 3D structure of the catalytic domain forms the active site, so the enzyme requires proper folding to be active. If you denature the enzyme, the catalytic domain will still be present (as this is a function of the protein sequence) but the active site will be gone.

As there are really many enzymes for all kinds of reactions it is hard to define a general form for the active site. A motif which is present in a lot of enzymes is the the form of a catalytic pocket or groove to which only the correct substrate of the enzyme has access. Additionally the binding of the substrate to the enzyme often induces a conformational change in the protein which closes this pocket. When the reaction is finished and the substrate is not bound anymore by the enzyme, the conformation changes again and releases the products of the reaction. See the image for a schematically drawing of this principle (image from here):


Are there biochemical differences between the cell membranes of prokaryotes and eukaryotes? I would like to know if there is any difference in chemical composition of cellular bilayer lipid membrane between eukaryotes and prokaryotes.

Specifically, I would like to know about the action of antimicrobial peptides on these bilayer membranes in context of the different membrane compositions.

It would be helpful if someone points me to some references.

There are differences. (Except mitochondrial eukaryotic membranes, which are indeed similar to bacterial membranes! (reviewed in van Meer et al., 2008)).

First, bare in mind that it is thought that even different eukaryotes, such as Fungi and Humans, have different cell membrane compositions and that this is reflected in the proteins (Sharpe et al, 2010). The outer membrane of Gram negative bacteria isn't even made of phospholipids, it's made of glycolipids (Kamio & Nikaido, 1976). Archean membranes have the most notable lipid compositions, including a bilayer-like monolayer, to adapt to the conditions they are found in (Oger et al 2013). My point being that saying "there are differences" is indeed an understatement.

This question has probably arisen because anti-microbial peptides seem to act with specificity, and that perhaps this specificity comes from direct peptide-lipid interaction. This is on the right lines. From wikipedia:

  The cell membranes of bacteria are rich in acidic phospholipids, such as phosphatidylglycerol and cardiolipin[23][27]. These phospholipid headgroups are heavily negatively charged. Therefore, the outmost leaflets of the bilayer which is exposed to the outside of the bacterial membranes are more attractive to the attack of the positively charged antimicrobial peptides.

Notably, no such charge exists in eukaryotes since the negative charge is found on the inner leaflet of the plasma-membrane rather than the outer leaflet.

There is such a massive variation, even within bacterial membrane composition (Bogdanov et al 2014), that I cannot even really begin to list it here. Furthermore, there are variations in the glycocalyx, surface proteins, and lipid composition dynamics due to lipid rafts.


Multiple numbers in the Ishihara test? When I was in high school (30 years ago), I took a biology class, and the instructor showed us an Ishihara color test for color-blindness. (This is the "hidden numbers" test.)

What I thought I saw once or twice was two different numbers* that had been embedded in the same slide. Were there slides in the test that had two or more numbers, or was I hallucinating?

[EDIT:] * "Two different numbers" means "different numbers in different colors."

The Ishihara Color Test consists of plates containing one number. But that number may consist of two digits (Fig. 1). After scouring the internet I have also found variants of the test where the each of the two digit had a different coloring (Fig. 2), but these tests may not all be validated/standardized or used by health care professionals. The plates may also contain one or two wiggly lines that have to be traced (Fig.1). In all, my conclusion is that there are many variants of this specific test around, at least on the web. I am not aware whether there are certain standardized versions being used by health care professionals. In all, my answer to your question...

  Were there slides in the test that had two or more numbers, or was I hallucinating?

...is that there might have been two digits of different coloring in the plate, dependent on the specific make of your teacher's plates. You might, or might not have been hallucinating. To give a more affirmative answer, the specific test with the specific make would have been dug up by your teacher.

Fig. 1. Ishihara test with a plate containing one number of two digits (left) and one or more wiggly lines (right). source: Colour Blindness

Fig. 2. Ishihara variants, showing two digits with different shades in the middle panel. source: allinesnowmop, a personal web page, credibility questionable


What species are these juvenile birds? What species are these juvenile birds found at São José dos Campos, Brazil?

The birds in question appear to be fledgling eared doves, which belong to the species Zenaida auriculata. The beak color, eye markings, and overall feather coloration were most indicative when IDing.

Here's a few images of what the doves may look like once matured:


Butterfly identification: Dorset England, July. Can you please identify this butterfly. It was seen in Dorset England 9th July. I think it is a female Silver Studded Blue.

The silver-studded blue is frequently found feeding on this plant, cross-leaved heath. There are good numbers of this species to be found on the heaths of Dorset in July and I would suggest that this is certainly silver-studded blue.


Do Black Hair Fuzzy Caterpillars bite? I saw a caterpillar in my bathroom. It's about 2 inches long and 3/4 inches in diameter. It has long (about 1 inches) long hair on his body.

I live in eastern India, Asia. I don't know if it was alive, as I didn't see any remarkable movement.

Are they dangerous? Do they bite? How to get rid of them?

I saw, it has long (about 1 inches) long hair on his body.

The hairs you refer to may be urticating hairs, which can cause extreme itching & irritation. Without a picture of the caterpillar, I can't say for sure though; out of extra precaution, let's just assume they are (until an image is provided).

  Are they dangerous?

As long as you don't let the caterpillar hair come into contact with your bare skin/body, there should be no risk of harm. That being said, be mindful of indirect contact; i.e., perhaps picking the caterpillar up with your shirt sleeve, the hairs now being on the sleeve, then you wiping your face with your shirt sleeve later in the day. See here for more information, including treatment, should said exposure ever occur.

  Do they bite?

Caterpillars do have the ability to bite, however, their bite isn't strong enough to pierce human skin. Nothing to worry about here..

  How to get rid of them?

To "get rid" of the caterpillar, I recommend getting a hard, thin surface - such as a piece of cardboard - ushering the caterpillar onto the surface, and then placing the caterpillar somewhere safe outside. If the caterpillar is in the process of molting, relocation can easily kill it, so please be diligent when attempting to relocate.


What’s the name of this tree? I’m trying to find information about this tree that I didn’t plant. Looking for information in terms of pruning, etc.

It had white flowers on it this spring, but is now flower less and has very few young berry-esque type fruits growing on it. They’re very small still, but it seems they’re going from green to a red. This in Michigan.

Additional pictures:

Thanks to Bryan Hanson for the answer! Found a picture online of it with flowers:

Revised Answer

The additional pictures point to something in the genus Prunus.  Note that there are extrafloral nectaries at the base of the leaves, and feathery stipules are visible (see here for annotated picture of a different species).  Since it has a weeping habit, and doubly toothed leaves, I think what you have there might be a Japanese Weeping Cherry Prunus subhirtella var. pendula (but other names seem to be in use).  Some info here which seems consistent with your specimen.

Original Incorrect Answer

I think you are probably looking at Ulmus glabra "Camperdownii" or a similar cultivar.  This is a "weeping" elm variety that is produced by grafting; all plants are descendants of a single tree. Wikipedia gives the full background.  Your specimen has somewhat more pointy leaves than many of the images for Camperdown Elm I found online, but apparently there can be some variation.

EDIT: The fruit picture (added after my answer) clearly rules out my answer!  Also looks like there are nectaries at the base of the leaves.


Does caffeine actually enhance cognition? I have heard, respectively:

Caffeine measurably enhances cognitive function.
Caffeine does not measurably enhance cognitive function in any significant way.
Caffeine enhances cognitive function, but only indirectly, in that it counteracts the effects of fatigue.
Caffeine enhances cognitive function, but only indirectly, in that it counteracts the effects of caffeine withdrawal.
Caffeine has no physical effect on cognitive function, but has a psychological effect.

What is the actual behavior of caffeine in relation to cognition?  (I'm particularly interested to know if any research addresses the claim that it only counteracts the effects of caffeine withdrawal)

Caffeine response is dependant on the individual. Caffeine has a very similar chemical make-up to adenosine which your body uses to transfer the energy you eat into energy your body can actually use (chemical energy). When your body has enough adenosine, it begins what is called a negative feedback cycle that stops adenosine production and sustains homeostasis. The feedback loops works by delivering a signal to put the body in a regenerative phase upon further adenosine binding. However, caffeine, being the wonderful individual that it is, disrupts that negative feedback loop and continues the conversion of excess (eaten) energy to chemical energy. But where in your body its dispersed is dependant on the individual.

The conversion to chemical energy is indirect though. Since adenosine is a principal neuromodulator, it actually tricks your body into behaving as it would at your most natural wakeful state. For example: Glutamate, GABA, norephinephrine, serotonin and acetylcholine are all inhibited by adenosine build-up at A1 receptors (a type of adenosine receptor) but caffeine stops adenosine from inhibiting these neurotransmitters. These five neurotransmitters all assist in metabolism (Glutamate is an essential compound in cellular metabolism).

Caffeine will never give you energy, it just uses your energy faster, in fact it probably causes energy debt from the work your body does to flush out the toxin.

In short: Yes it can enhance cognition, if the extra ATP (energy molecule made from adenosine) is carried to the brain. As it is not a homeostatic process it's difficult predict.

When the body is constantly put out of it's homeostasis, it adapts the toxin into its homeostatic balance (kind of like a beat em' or join em'). In this way, an individual's body begins to need the caffeine to function normally. Caffeine dependance is very low however, since it has been around for centuries, we've evolved to know it as a toxin but to not depend on it.

References:

J Alzheimers Dis. 2010;20 Suppl 1:S3-15. doi: 10.3233/JAD-2010-1379.

http://thebrain.mcgill.ca/flash/a/a_11/a_11_m/a_11_m_cyc/a_11_m_cyc.html

http://pharmrev.aspetjournals.org/content/51/1/83.short


Flowers sent by the birds Birds have sown seeds on my ground and this beautiful flower has sprung.  What's the name of this flower?

I live in Sao Paulo, Brazil

It's a type of begonia. With 1800 species in the genus, it's hard to say which it is, but the leaves which seem palmate would place it in the aconitifolia species. Your leaves don't appear to be variegated, and your flower is deeper pink, but it's the same flower species.


Whence fecal E. coli (et al.) if swallowing it is dangerous? I don't know much about medicine, and I know even less about microbiology, but I understand that there are organisms in the lower gastrointestinal tract (and in feces) of a human, like Escherichia coli, that can cause dangerous disease if swallowed (or injected intravenously) by a human. So how did they get to the lower gastrointestinal tract in the first place? I assume either (or some combination of)

its prevalence in feces is less than I'm led to believe, so my question as to how it got there doesn't arise;
the percentage among cases of swallowed E. coli of those that lead to disease is low; or
E. coli-caused disease is more common than I'm lead to believe.

Does anyone know which of these is true? Or is it something else? (Perhaps they enter the gastrointestinal tract from below and not via swallowing?)

E. coli is mostly harmless; only a few strains are harmful.

I don't believe the route by which gut biota is established has been entirely established for any species but, for example, koala feed their faeces to their offspring to help them establish biota capable of digesting eucalyptus. It seems that a small proportion of ingested bacteria somehow survive passage through the stomach to the gut and then begin multiplying and colonising the intestines.

It's also important to realise that just because an organism is sometimes harmful doesn't mean it always is. There are many microorganisms that are pretty much ubiquitously found on or in your body which are capable of causing disease but only do so very rarely; usually when the body's defences have already been compromised (e.g. Pseudomonas aeruginosa, Candida albicans aka thrush, and so on).


Can radiation exposure cause cancer later in life even if no traces of radioactive material are present in the body anymore? I had a long-lasting debate with a friend of mine about the Fukushima incident.

The question that we tried to solve was if radiation or toxin exposure can cause cancer later in life even if no traces of radioactive material or toxins are present in the body anymore.

Yes it can, because exposure alone can cause mutations in your genes which is usually the main cause of cancer.

For example, when we get exposed to UV light for longer periods of time, we can get skin cancer/melanoma. Here , of course no traces of these rays are present in our body, its just all due to prolonged exposure.

Now to the fact that why does it even happen , according to wikipedia is

  Cancer is a stochastic effect of radiation, meaning that the probability of occurrence increases with effective radiation dose, but the severity of the cancer is independent of dose. The speed at which cancer advances, the prognosis, the degree of pain, and every other feature of the disease are not functions of the radiation dose to which the person is exposed.

So since once induced, it just keeps on increasing even though you are not exposed to that particular rays anymore, you most probably are going to have it. This is the reason why cancer is so dangerous, because once it is there you can't stop and even can't make any precise stats about it until a certain stage.

For more details , visit https://en.wikipedia.org/wiki/Radiation-induced_cancer#Mechanism

I hope this answer helps you :)


If I workout, will this inherited trait (of being stronger) not be passed down to my offspring (Lamarck's theory on evolution)? I'm a student in biology and just recently learned about Lamarck's theory on evolution and how it has been disproved. While I understand that you cannot alter your genes, I'm still having a hard time understanding some parts of it, mainly how inheriting strength (such as working out) will not be passed down to my offspring. If someone was obese, exercised to the point of no longer being obese, will this person's offspring still start off as obese?

Indeed, whether you work out or not will not change how strong your offspring will be. This is exactly why Lamarck's was wrong.

I would note however that Behaviour can be heritable and Your behaviour can affect your kids environment

Behaviour can be heritable

The probability of you working out is affected by your genes and so if you have a genetic predisposition for willing to work out, this will be passed on.

Assuming there are genetic predisposition for liking to work out, the fact that you worked out would not increase the probability of your kid to work out via genetic inheritance but the fact that you have a genetic predisposition for liking to work out will increase the probability that your kid will have the same preference and will work out

By the way, if you want to learn more about the concept f heritability you should have a look at Why is a heritability coefficient not an index of how “genetic” something is?

Your behaviour can affect your kids environment

Working out won't affect your genes but it will likely affect the environment in which the kid will grow. Here are three examples

Teaching

If you eat healthy, you will probably teach your kids to eat healthy too.

Womb environment

Also, if you eat healthy and are a woman, you will likely give the right nutrients to your offspring while still in the womb (assuming you are a lady).

Epigenetics

Your environment will cause epigenetic changes (changes not in DNA but in the very close environment of the DNA such as typically histone tail methylation). These epigenetics modifications will be directly passed to the foetus.

More information

A post your question is almost a duplicate of...

Is it the case that all changes in phenotype during life are not inheritable?

A post on heritability

Why is a heritability coefficient not an index of how “genetic” something is?

And finally an answer that talks about non-genetic inheritance

Why does evolution only involve heritable traits?


Possible reasons for DNA getting stuck in well I am in the process of Library preparation for Illumina MI-Seq using mtDNA. Using NEB Hotstart LongAmp Polymerase, I was able to obtain upto 10kb amplicons of mtDNA. However, when I switched to a different DNA sample, I am not noticing bands anymore in the gel. Strange thing is that, if I fragment these samples (Diagenode Bioruptor acoustic shearer) I get fragmented smears similar to the ones I expect from fragmenting a 10kb amplicon, even though these are stuck in the well.
Therefore, I dont know if a 10kb amplicon is stuck in the wells and is not migrating (given I see similar results for fragmentation for the samples that got stuck), or I am seeing in the wells what is genomic DNA and no amplification has occurred. Does the 260/230 value affect PCR amplification in any way? (I have a very high 260/230 value ~5 for the new DNA sample I am using)

There is one simple reason for that, your agarose gel is most likely too dense. Depending in the type of agarose, I would prepare a 0.5-0.6% gel at maximum.

Synbio gives this list for "standard" agarose, which fits pretty good with my experiences. If you use low melting agarose, this table looks a bit different, as the gel matrix is not a dense. The disadvantage is that the gel is much more prone to get damaged while handling.


What is the purpose of the AraC gene in pGLO? The AraC gene activates in pGLO from my understanding in the presence of arabinose. Arabinose is present as a metabolite from other metabolic in the e.coli cell. Is it that there's no termination marker, so transcription continues to the GFP gene?

In addition, does AraC contain parts that are encoded 5'->3' and 5'->3'?

The AraC gene can activate GFP expression, because the GFP in the pGLO plasmid has the negative inducible pBAD promoter:
In the absence of arabinose an AraC protein dimer binds the promotor region, but does not activate transcription. When arabinose is present, the protein binds in a different way, which allows the downstearm gene (here GFP) to be produced.

According to this plasmid map I found the AraC and GFP genes are in different orientations (and facing 'away' from each other), so transcription of AraC wouldn't run over into GFP even without a terminator present.


How harmless bacteria on skin defence against harmful bacteria? I have read that there are some harmless bacteria live on skin and they also have role in protecting body against some harmful bacteria but how do they do so? I mean how these bacteria are able to resist other bacteria which are harmful?

Relations between organisms in complex ecosystems are various, so I won't give an exhaustive answer, only keys to understanding.

First, you need to consider that a bacterium harmful to humans is not necessary harmul to other bacteria. So there is no reason why our skin microbiota will only target/resist to human pathogens.

What's more, microbes are not inherently harmful to us. Their dangerosity also depends on the capacity of the skin to block them 1.

Then, microbial defence mechanisms depend on the kind of relation they have to the potential pathogen: competition, parasitism, predation, etc.

The article cited below will give you a nice overview on the topic.

1 Cogen, A. L.; Nizet, V.; Gallo, R. L. (2008) Skin microbiota: a source of disease or defence? British journal of dermatology, 158, 3, 442-455; doi: 10.1111/j.1365-2133.2008.08437.x


What is the role of Aspartate Transaminase in gluconeogenesis? I know that oxaloacetate cannot cross the mitochondrial membrane, but can instead be converted to aspartate, shuttled out, and then re-converted back to oxaloacetate.  What does this have to do with gluconeogenesis?

The traditional route is to convert pyruvate to OAA to malate in the mitochondria, shuttle the malate out, and then convert malate back to OAA in the cytosol.  If lactate is the precursor, then the conversion of lactate to pyruvate in the cytosol can generate an NADH, making the conversion to malate in the mitochondria unnecessary.  Thus, OAA is converted directly to PEP in the mitochondria by mitochondrial PEPCK and shuttled out to the cytosol to begin gluconeogenesis.

If we have these two pathways, what is the point of using aspartate?

I may have approached this problem from the wrong direction, so here's my attempt at an answer:

For gluconeogenesis to function, glycolysis needs to be shut off.  Glycolysis feeds the TCA cycle with Acetyl-CoA through the decarboxylation of pyruvate, and without glucose as a source, we need to look to other methods of generating OAA to make into PEP.  We can make OAA through Aspartate Transaminase by reacting Aspartate with α-ketoglutarate.


Nucleosome wrapping direction Does anyone know which direction the nucleosomes are wrapped? I wonder:

Relative to the B-DNA double helix twist direction (right-hand)
Relative to the neighbor nucleosomes. Do they alternate to prevent supercoiling?

B-form DNA is wrapped around histones in a left-handed manner resulting in a left-handed solenoidal superhelix (see that, that and this). The reason for this wrapping is that it reduces the helical tension. This post has more information about DNA helical tension. Also note that exceptions exist (i.e. right-ended direction) especially for histone at the centromere as described in this paper.

For your second question, the exact way nucleosomes are then arranged to produce the chromatin fiber is, as far as I know, still not fully understood but the most accepted model is a zigzag arrangement (Woodcock CL & Ghosh RP, 2010 and Grigoryev SA & Woodcock CL).


Why does Glutamine have the symbol Q? Spent a half hour googling this and the best I could find was this:

  Now for some rhymes: Arginine = R. R we having fun yet?
  Asparagine = N The kNights of Ne say "Ne".
  Glutamine is a cute amine = Q
  I say "glutamate"/a former vice president says "glutEmate" = E
  ditto with AsparDic acid = D
  Fenylalanine makes tasty italien sausage = F
  Theres are two rings in tryptophan, and there are two v's in W = W
  Tyrosine = Y, Y? Because we love biochemistry. Source: One letter codes, rhyme and reason

Initial letters of the names of the amino acids were chosen where
  there was no ambiguity. There are six such cases: cysteine, histidine.
  isoleucine, methionine, serine and valine. All the other amino acids
  share the initial letters A, G, L, P or T, so arbitrary assignments
  were made. These letters were assigned to the most frequently
  occurring and structurally most simple of the amino acids with these
  initials, alanine (A), glycine (G), leucine (L), proline (P) and
  threonine (T).

  Other assignments were made on the basis of associations that might be
  helpful in remembering the code, e.g. the phonetic associations of F
  for phenylalanine and R for arginine. For tryptophan the double ring
  of the molecule is associated with the bulky letter W. The letters N
  and Q were assigned to asparagine and glutamine respectively; D and E
  to aspartic and glutamic acids respectively. K and Y were chosen for
  the two remaining amino acids, lysine and tyrosine, because, of the
  few remaining letters, they were close alphabetically to the initial
  letters of the names. U and O were avoided because U is easily
  confused with V in handwritten material, and O with G, Q, C and D in
  imperfect computer print-outs, and also with zero. J was avoided
  because it is absent from several languages.

  Two other symbols are often necessary in partly determined sequences,
  so B was assigned to aspartic acid or asparagine when these have not
  been distinguished; Z was similarly assigned to glutamic acid or
  glutamine. X means that the identity of an amino acid is undetermined,
  or that the amino acid is atypical. "Nomenclature and Symbolism for Amino Acids and Peptides"


Determine which seed will germinate first I recently studied about plant physiology for a test. Strangely, there was this question which I had no idea how to approach.

The question is,
Which seed will germinate first?

a) Castor
b) Wheat
c) Mung( Vigna radiata )

The answer is (c). I want to know how do we determine if which seed will germinate first? Which factors does it depend upon?

You'd have to know the individual germination times for each family.  I'm linking a table for vegetables, but it doesn't include the three plants you're looking at.  A google search for each one individually shows that yes Mung does have the shortest germination time.  It's a memorization question.

To add to that here is a paper where they review variation times between over 600 seeds and find that the variation in time is mainly constrained within families.


What determines testosterone exposure in womb, baby's genetics or mom's body? I read this article which has the following quote:

  The ratio between index and ring finger is believed to be linked to exposure to the male hormone testosterone in the womb.

And I wonder what determines the amount of exposure to testosterone in the womb. Is it testosterone produced by the fetus itself, in which case the baby's own genetics is the answer, or does this exposure the article speaks of more likely refer to testosterone produced by the mother and exposed to the baby?

Fetal testis produces testosterone from cholesterol. There is a peak of production around 15 weeks of gestation (the "masculinization programming window"). So the genotype of the fetus can affect testosterone levels directly via effects on the biosynthesis of the hormone, or indirectly by defective regulation of the pathway's activity.

However, exposure to chemicals in the mother's environment is also thought to play a part in determining testosterone levels. The classic example of this is the phthalate esters used as plasticizers.

  Scott et al. (2009) Steroidogenesis in the Fetal Testis and Its Susceptibility to Disruption by Exogenous Compounds. Endocrine Reviews 30: preprint freely available here.


Why we do not use RNAi to control ebola? As you know using RNAi we are able to prevent gene expression. so why we do not use it to stop viral genes expression?

Delivering siRNA in vivo is a difficult prospect, but has been overcome in research environments and several commercial in vivo solutions are on the market see examples from Life Technologies here.

The bigger problems come from potential off-target effects. siRNA tend to be double stranded and both the 'guide' and 'passenger' strand can occasionally target multiple sequences that you did not intend. Additionally, siRNA tend to activate the body's immune system in ways that would inhibit therapy or cause excess inflammation and cell death. See the detailed review here.

In short, it is a good idea, and the current research in the field is working to overcome technical challenges, but we are not there yet.


Do other young mammals turn their backs to their parent when upset? I have noticed that upset toddlers turn their back to someone who wronged them and huff. Most adults don't do this, so I don't know how this could be a learned behaviour. Do other animals express this behaviour? I do not see how this could be specific to culture.

Other Primates
Sulking is the behavior you are refering to and it is seen in orangutan, Chimp and Bonobo. Likely in other primates but I am not aware of any published works. I have heard about it in baboons but have not read the papers myself.
Source
Source2
Source3
Source4
Also adult humans DO do this on occasion, it is just often more subtle.
It is amazing how many identical social behaviors are seen in our close relatives, especially the ones about conflict and conflict resolution.


Does electricity cause damage on a cellular level? As I understand it the mechanism of death when a mammal is electrocuted is that the current disrupts the SAN/AVN in the heart causing it to fibrilate or arrest.  That's on a macro scale, however.  What damage, if any, does electricity cause on a cellular level?  I've noticed some sort of moss or lichen growing on the third rail of the train lines so I'm aware that they must be able to cope with the current, do they have adaptations ot allow this or is it just that they are not connected to the earth?

Regarding the moss or lichen on the third rail on British train lines: there is no current passing through the moss/lichen as they are not completing a circuit. They are just sitting on one connector. If another connector passed over them, completing the circuit across them, then a current might pass across them for a very short time. But I doubt they grow on the top of the rail (which is the contact part in the UK system) as that is constantly being polished smooth by the contacts from trains sliding across it.

Regarding cell damage: Apart from fibrillation in animals, and burns caused by Joule heating, electricity does cause cellular damage.

At low frequencies (<10kHz), electricity disrupts cell membranes and makes them much more permeable (we actually harness this when we use electroporation to transform bacteria). All organisms rely on electrochemical potential differences across membranes for their metabolism (Berry, 2002). The exact effect is dependent on the previous electrical state of the cells, for example the electrical potential difference across the membrane, and on the surface area to volume ratio of the cell (greater volume relative to surface area leads to more disruption). In any case, extreme electroporation can cause solutes to flow in or out of a cell, and generally disrupt the balance of solute concentrations and cause organelles and other bodies to move out of a cell. When the electrical stimulation stops, the contents are then fixed in a disrupted state. The cell then has to expend enormous amounts of ATP using ion channels and transport proteins in an attempt to reinstate the necessary chemiosmotic potentials, and in doing so exhausts the entire ATP supply and goes into biochemical arrest (no metabolism occurs), which is when a cell is dead. Dead cells break apart because there are is no maintenance occuring.

At higher frequencies (10-100kHz) proteins become permanently denatured. Many proteins carry charges which give them an overall polarity. When placed in an electric field, the proteins reorient themselves and will undergo conformational change to achieve the optimum dipole moment in the direction of the field. Ion channels and pumps are particularly sensitive to these disruptions (since their charges are crucial to their function).

Rather than provide lots of references, there is one excellent review from which I drew all this information, and which you should read for more of the physical detail (Lee et al., 2000).

References:

Berry, S. (2002) The Chemical Basis of Membrane Bioenergetics. Journal of Molecular Evolution. [Online] 54 (5), 595–613. Available from: doi:10.1007/s00239-001-0056-3 [Accessed: 9 February 2012].
Lee, R.C., Zhang, D. & Hannig, J. (2000) Biophysical injury mechanisms in electrical shock trauma. Annual Review of Biomedical Engineering. [Online] 2 (1), 477–509. Available from: doi:10.1146/annurev.bioeng.2.1.477 [Accessed: 9 February 2012].


Can bacteria only thrive in agar solution? In petri dish, agar is most commonly used for culturing bacteria. So is there any other easily obtainable food sources for culturing bacteria.

You seem to have some misconceptions about growing bacteria. These are cultivated using specific media, for E.coli this is usually LB Medium which contains the following ingredients per liter:

10g Bacto-tryptone
5g yeast extract
10g NaCl

This is dissolved in water and subsequently sterilized by autoclaving. Note that there are much more medium recipes for different strains and different culturing conditions.

Bacteria can then be grown either in suspension (shaking in an Erlenmeyer bottle in the liquid media) or on the surface of plates. To produce these plates, you need an agent, which solidifies the medium without having any effect on the growth of the bacteria or the medium. And this is where the Agarose is used. It can be heated up with the medium during sterilization, does not interact with the medium and bacteria do not metabolize it. If you cultivate bacteria, which produce agarase (which is an enzyme to break down agarose), you need to use a different agent to solidify your medium. And you will use a different medium anyways.
They simply grow on the surface of the solified medium and can easily be picked for further analysis or the inoculation of (bigger) liquid cultures.


When the leaf length ranges are given in a plant species' description, what do the numbers in parentheses represent? Referring to a plant species, a paper I am reading (see citation below) says: "Blades are 4–5(6) mm long and (0.5)1–1.5 mm broad."
I understand the numbers 4-5 and 1-1.5 would be the ranges, but what do the numbers 6 and 0.5 in the parentheses represent?
Domínguez, Y., Valdés, C. M. P., & de Miranda, V. F. O. (2012). New features of Cuban endemic Pinguicula filifolia (Lentibulariaceae) and considerations on its habitat and ecology. Flora-Morphology, Distribution, Functional Ecology of Plants, 207(11), 838-841.

Anytime you see this being used in terms of a range...

the numbers outside the parentheses represent the normal or expected range, and

the numbers inside the parentheses represent atypical extensions beyond the normal range that are uncommon but possible and recorded.

Radford, Ahles, and Bell's 1968 flora, Manual of the Vascular Flora of the Carolinas confirms this in its preface (page vii):

In instances where most measurements for a character fall within one part of the total range of variation, the more infrequent or extreme size range is given in parenthesis as an extra measurement: e.g., "leaves 4-8 (16) cm wide", not "leaves 4-16 cm wide."

So, in your example, you can interpret the first range as follows:

Blades are typically 4-5 mm long (but sometimes 6 mm long) and typically 1-1.5 mm broad (though sometimes only 0.5 mm broad).

 Radford, A.E., Ahles, H.E. and Bell, C.R., 1968. Manual of the vascular flora of the Carolinas. Univ of North Carolina Press.


What are some useful (starter) metrics to use on phylogenetic trees? I'm doing a computational biology project in which I simulate evolution under different inheritance rulesets and I am generating phylogenetic trees (beautifully visualised in Python with ete3).

My question is: where can I find and test out some simple metrics that can describe these trees in terms of 'branchy-ness' (you can tell I'm not a bioinformatician or phylogeneticist!). I'm looking for kind of mean-field descriptors of the trees. Kind of like degree distribution for networks.

My specific goal is, like in network science, trying to see if I can differentiate between different rulesets that created the tree by examining the [statistical] properties of the tree itself.

Here are a few metrics you can calculate to get you started. You can use R to perform these calculations.

Net Diversification Rate (r)

Net diversification rate is (rate of speciation - rate of extinction). You can calculate it using the bd.ms or bd.km functions in the geiger package for R.

r = 1:

r = 2:

Tree Imbalance: Colless index (I)

Colless's index measures how imbalanced the tree is. It sums the differences in the number of clades in each pair of taxa. You can calculate it using the colless function in the apTreeshape package for R.

I = 0

I = 21

Branching Times (gamma)

The gamma statistic measures how much later or earlier branching times happen than what you would expect from a normal birth-death process. A negative value means branching times occur earlier, positive means branching times occur later. You can measure gamma (and generate a lineage through time (ltt) plot, as shown below) using the ltt function in the R package phytools

(From this Nature article)

These are just a few of many parameters you could calculate for a phylogenetic tree. It should be enough to get you started.


Where do I find standard tissue and cell names? I am developing specialized database on some desease microarray experiments. The initial data is retreived from NCBI and ArrayExpress databases. The problem is that sample attributes sometimes specify similar or same things but in different manners: as cell and tissue names, desease names, age, ethnicity of donor, ect. Where do I find conventions for naming experiment sample attributes?

It turns out that ArrayExpress itself uses various ontologies (dictionaries structured as trees) available at Ontology Lookup Service when it processes users' search queries. Experimental Factor Ontology is the precisely one I was searching for.

Medical Subject Headings (MeSH) dictionary turned out to be handy as well.


Applications of shortest path problem The shortest path problem is the problem of finding the shortest path between multiple nodes. What are the applications of the shortest path problem in biology?

A simple google search gives me this - http://mutage.oxfordjournals.org/content/30/2/191.full.pdf
This, unfortunately is under a paywall.

Apart from that article, I can't find anything else useful.

The classic application is analysis of graph data. For example, protein-protein interaction networks or gene regulatory networks and the like. There are various types of data that can be presented in the form of a network and network analysis is an integral part of Systems Biology.

Another example is determining the similarity of functional annotations from the Gene Ontology. One of the ways of doing so is finding the shortest path between two nodes in the GO graph.

Or, for a more concrete example, I recently published a paper where I examined various features of a particular group of proteins. One of the pieces of information I used was how central these proteins were to the network and, for this, I measured how often they served as a node in the shortest path between two others.

The simplest way for you to find more example is to go to PubMed and search for "shortest path":

https://www.ncbi.nlm.nih.gov/pubmed/?term=shortest+path


What is the difference between these worms: Caenorhabditis elegans and Eisenia fetida? I love worm composting (I use red wiggler worms), but wondering how similar or different the Caenorhabditis elegans and Eisenia fetida are?

Caenorhabditis elegans is a nematode. Eisenia fetida is an annelid. They both are lophotrochozoans (more specifically, trochozoans).

Time of Divergence

According to Michael Lynch, there are about 41 amino-acid substitutions per site between Annelida and Nematoda. According to Lynch's data, I estimated that this difference is roughly equal 100 million years.

Therefore, assuming the rate of molecular evolution was constant, their common ancestors lived about 100 million years ago.

Difference on Anatomy

Nematodes have pseudocoelom while annelids have eucoelom. Therefore nematodes do not have a vascular blood system. However, annelids do have one. Nematodes also lack a layer of circular muscle, which annelids have. This layer of muscle allows annelids to move by shorten and elongate their bodies.

C. elegans in particular does not have a female gender. There are only male worms and hermaphrodite worms. Only the male can fertilize other worms.

E. fetida is hermaphroditic and two of them can fertilize each other.


What are the typical values of probabilities for nonspecific binding to an antibody? I'm physicist by training, so please excuse me if I don't use the proper terminology.

I think there is a way to make a sensor that detects if a single antibody has caught something from the flow. So I'm trying to figure out if this would be a useful sensor, but this depends on how specific the antibodies really are.

When I ask biologists "How specific are antibodies?", they reply: "Very-very specific", but provide no values that I understand on microscopic level. But I am trying to make a quantitative estimation, e.g. for the following thought experiment:

Suppose I have attached an antibody to inorganic surface. It's an antibody for catching object X. And I flow blood over the surface, slowly. Suppose there's no X in this blood at all. But there are lots (maybe 1017, or some crazy number like that) of other stray particles flowing by this antibody every second, right? So, when one of these particles bumps into this one antibody, what is the probability that it would stick to this antibody? Is it really 10-17 ? Is it really so small?

And, in any case, how do I estimate this probability at least to 1-2 orders of magnitude?

Also, how do I estimate the "collision cross section area" through which an object has to fly to make an attempt to bind to an antibody? In other words, does it only have to touch it slightly, or bump into antibody in a hard and messy collision?

Does the probability of successful bind depend on the flow speed?

How would the values change if I take serum instead of blood?

Could you please point to some relevant papers, books or just keywords? I would very much appreciate any help.

TL;DR Specificity of antibody can be not superb. It can give false-positive results in up to 90% of experiments. However, some essay are 90% specific.
That is an interesting question and there sure a lot of research done to understand specificity and strength of binding of antibody to its target.
First of all, let me say that antibody-epitope interaction is, as many biological processes, probabilistic process, which means it can go either way, however, after binding antibody need a lot more energy or time to "fall off". Direct contact is always required for establishment of non-covalent bond between antibody and epitope, because characteristic length of that interaction is very low (order or angstroms, 0.1nm and less). Point here is that you don't need to run antibody in stream, rather let is sit in solution with your sample or mix gently, random thermal motion will take care of them finding each other. In flow you will waste a lot of antibody, which is expensive.
I think that you can estimate probability of given antibody binding given molecule from their 3D structures, but this is extremely burdensome calculation. What you can do experimentally, I suppose, is label "right" epitope with red fluorescent tag, and every other molecule in your solution with green tag. Then run solution through column with antibody sitting on beads (as in chromatography), elute everything and compare green to red signal. Measuring accurately, this will tell you how much "junk" antibody picked out of solution.
Now, to numbers. Here Abcam talks about its antibody for progesterone. Molecules, closely related to progesterone, are recognized with 40-90% efficiency, compared to true-positive target (progesterone). But this is absolute-worst case scenario, because those molecules are so closely related.
On other note, antibody specificity is very important when essay is used, e.g. for HIV diagnosis. Here is nice page from U Penn, that discusses issues with specificity:

For example, in one study of 290,000 asymptomatic Minnesota blood donors donating 630,000 blood units, the false positive rate when both the screening and confirmatory assays were positive was was 0% per donation (95% confidence interval 0% to 0.0006%).
...
For example, in one study of asymptomatic Italian blood donors, only about 13% of donors with repeatedly-reactive EIA tests were confirmed to be HIV-infected on the basis of positive immunoblot. However, in a high risk population the false-positive rate can be much lower, as low as 1-3%.

I couldn't find any more precise data or studies. In biological imaging (my field) antibodies are split into "works" and "don't work, drop it" (aka high background) groups.


Does RNA polymerase move around DNA or does DNA rotate beneath the polymerase? I'm thinking of the human genome specifically, but more general answers are welcome.

As RNA polymerase moves along the DNA helix it follows a single strand.  The two DNA strands are unwound locally by a helicase enzyme. However, after some distance, I imagine that either the polymerase must move around the axis of the DNA OR the DNA must somehow be rotated along it's length to relieve the twisting by the polymerase.

I can't quite understand how the DNA is free to rotate, being part of a very long molecule. However the other option is also causing me a problem: the growing (nascent) mRNA can be tens of thousands of bases long while still attached to the RNA polymerase and the DNA template.  If the RNA polymerase follows the helix of the DNA, does it also drag the full transcript around with it?

Both the DNA and the RNA polymerase complexes moves along the DNA molecule like it was a track. While the new mRNA is big, it would never be as big as the whole genome, so the reference point is the DNA molecule. Plus, the functioning of the movement of this enzymes is quite similar to other proteins that move "climbing" long polymers, such as actin polymers or microtubules.

One of the theoretical models that describes the movement of this kind of proteins is the model of rectified thermal diffusion, based on Richard Feynman's idea of the Brownian ratchet. A Brownian ratchet is a device that allows the conversion of Brownian random movements into a directional force.

http://en.wikipedia.org/wiki/Brownian_ratchet

The polymerases consume ATP, which enable them to suffer cyclic conformational changes (one change per ATP consumed), which allows the complex to attach to the molecule and detach. Once the complex has detached, by simple diffusion it moves in a random direction. Then, it attaches again. If the movement has occurred in the right sense, it will stay where it ended, while if it has gone in the wrong sense it will return to its previous position. As only a few movements are allowed, the complex will only move in that sense, even if the motor force is random.

I don't know exactly what conformational changes occurs in the RNA polymerase, but this general process seems to apply to almost any motile protein, including those enzymes that travel across polymers. Since the motor force is simple diffusion, and since the mRNA molecule doesn't need to "travel" with the polymerase (it just floats joined to it, but doesn't "pull"), I think there isn't any trouble with this.


How do cells determine what size to grow to before dividing? How do cells determine size to grow to before dividing?

All eukaryotic cells have 'checkpoints' during their cell cycle (1)1. They will only commit to cell division or the next phase of mitosis until all requirements have been fulfilled. The cell needs to have enough energy and the right external stimuli before it starts the irreversible commitment to cell division. The proteins effecting these changes are the cyclins and the associated CDK's. These proteins integrate a wide array of signalling inputs (e.g. DNA duplication complete or no major DNA damage) and steer the proteins actually duplicating the DNA and the other machinery needed to split a cell. You can learn more about these proteins and their signals by googling 'restriction point'

If you interfere with cyclin D modifying proteins you can get very large or very small cells. One of the best understood proteins involved is WEE1 from fission yeast. If you knock this one out, you get very small cells (2).

In mammalian cells the size of the spindle during anaphase also seems to be crucial in splitting cells equally (although some divisions are asymetrical)(3).


What insect is this? (England) Found this in my room and haven't seen anything like it before. It was about 4-5cm long and has wings. Flew away before I could get a better picture.
Photo taken from the Midlands, UK

I think i have an answer it is this nice guy.

Latin name is Leptoglossus occidentalis.

Short description of Leptoglossus occidentalis:

  Western Conifer Seed Bug
  The Western Conifer Seed Bug Leptoglossus occidentalis is a large and conspicuous squashbug, reaching a length of 20mm when adult. It is easily distinguished from all other GB coreids by its reddish-brown body, transverse white zigzag line across the centre of its wings and characteristic leaf-like expansions on the hind tibiae.


Earliest to use media after autoclaving? I am autoclaving media to use later to inoculate yeast. How much time do I have to wait before using the media and adding the culture? Can I use it a few hours after autoclaving?

There is a relatively simple (and yet logical) answer: You can use the media as soon as they are cold enough for your desired culture temperature. So if you want to use the media at 30°C, there is no need to wait longer. The media will only warm up again in the incubator until this temperature is reached.

The addition of antibiotics is also uncritical, since the media is ways to hot to be directly used when they still inactivate antibiotics. Your cells wouldn't survive this either.

There is also no waiting period necessary to use fresh media after autoclaving, since there are no processes going on when the autoclaving was done properly. If not, you will see contaminations pretty fast.


Definition of Sexual Selection? How do you define Sexual Selection (SS)?

(One might want to subdivide SS into intra- and inter- SS to answer)

Is SS clearly different from Natural Selection (NS)?
Is SS nested within NS or are NS and SS two different and (anti- or not) parallel processes?
Is the evolutionary processes due to sexual conflict are SS processes?

  Sexual conflict arises when the reproductive interests of males and females are not aligned, generating sex-specific selection on shared traits such as mating rate (from this article)

  (One may want to subdivise sexual conflict into intralocus and interloci conlict to answer)

  Are the evolutionary processes of sexually antagonist genes SS processes?

  Sexually antagonist genes are those genes where one allele is favored in females while another allele is favored in males (my own definition)

Can SS be accurately defined or is there a continuum of kinds or processes from complete SS processes to complete NS processes?

Stated differently, is SS defined as the color orange (it is a continum) or like a square and a rtiangle (no continuum)
(I talk here about kinds of processes, not about the relative importance of SS and NS in explaining the evolutionary dynamic of a trait or a locus)

If you define SS based on some other concepts that might be subject to various definition, please define this other concept. For example, if one says "SS occurs on a trait whenever this trait undergoes directional selection due to sexual competition", he will necessarily need to define "sexual competition" as well.

Below is a list of scenarios where you can answer by yes or no whether SS is involved in the evolution of some feature. In all of these scenarios, we'll consider cases where the males have to find a mate…

The males need good ears to find the females before other males. Is SS involved in the adaptation of ears abilities?
The males need good flying abilities (supposing we talk about flying animals) to have access to females before another male. Is SS  involved in the adaptation to good flying abilities?
The males need good flying abilities  to have access to females although there is not much between male competition because the vast majority of females won't never be fertilized. Is SS is involved in the adaptation to good flying abilities?
The males need good flying abilities to be able to fly a long time without spending to much energy otherwise they will die before finding a female. Is SS is involved in the adaptation to good flying abilities?
The males need good flying abilities to be able to fly a long time without spending to much energy otherwise they will die before finding a female. There are quite a few females but there the competition is so rough to find a female that is still unmated Is SS is involved in the adaptation to good flying abilities?
The males need good camouflage because when they fly to find a mate they may get eaten by a predator and die before reproducing. Is SS is involved in the adaptation to good flying abilities?
The males need good camouflage because when they fly to find a mate they may get eaten by a predator and die before reproducing. Here the difference is that the predators are attracted to the spot if they can sense many males. So the presence of the other males influence the probability of finding a mate of a given male. Is SS is involved in the adaptation to good flying abilities?

Is SS clearly different from Natural Selection (NS)?
Is SS nested within NS or are NS and SS two different and (anti- or not) parallel processes?

Darwin, in The Descent of Man, and Selection in Relation to Sex defined sexual selection as a type of selection that "depends on the advantage which certain individuals have over other individuals of the same sex and species, in exclusive relation to reproduction." Throughout, he distinguishes between natural and sexual selection. This suggests to me that Darwin thought of them as different processes.  A spot check of various evolutionary texts show the authors all using some variation of Darwin's definition.
In my opinion, the two are are clearly different but not necessarily separate. Both NS and SS affect fitness, a major component of the evolutionary process.  I tend to think of SS as nested within NS. NS affects fitness indirectly. Beneficial traits increase survivorship.  The longer individuals survive, the more reproductive opportunities they will have and fitness will, on average, increase. But, survivorship does not guarantee reproduction. Thus, I think natural selection acts indirectly on reproductive success.
SS operates directly on reproductive success because males selected by females will reproduce, increasing their fitness. Sex is, after all, a natural process. In my view, female choice is the "environment" of the male (as far as reproduction) so variation of male traits in the female choice "environment" differentially affects the fitness of the males. That is natural selection.

Is the evolutionary processes due to sexual conflict are SS processes?

Absolutely. Sexual selection ultimately arises because of a difference between genders of energy investment in gametes. Males produce lots of gametes and relatively little energetic cost. Females produce relatively few gametes with lots of energetic cost (think of tiny sperm vs large, yolk-filled eggs). It benefits males to mate with as many females as possible because, even if a mating produces no offspring, he lost very little of his energy investment. Females will be choosier because they can't afford to waste gametes. Thus, there is an inherent conflict of interest between males and females.

Are the evolutionary processes of sexually antagonist genes SS processes?
Sexually antagonist genes are those genes where one allele is favored in females while another allele is favored in males (my own definition)

Are these genes related exclusively to reproduction?  If so, then that would be consistent with the original concept of SS. However, sexually antagonistic genes are not necessarily the result of or a cause of SS.  For example, Rice (1992) argued that sexually antagonistic genes may explain the evolutionary reduction of recombination between primitive sex chromosomes.
Rice, W.R. 1992. Sexually antagonistic genes: Experimental evidence. Science 256: 1436-1439.

Can SS be accurately defined or is there a continuum of kinds or processes from complete SS processes to complete NS processes?

I think SS is accurately defined, but whether is is a type of NS or not is (I think) open for debate. As I described above, I think of SS as a particular type of NS, one that operates directly on reproductive success rather than indirectly.

Below is a list of scenarios where you can answer by yes or no whether SS is involved in the evolution of some feature. In all of these scenarios, we'll consider cases where the males have to find a mate…
The males need good ears to find the females before other males. Is SS involved in the adaptation of ears abilities?

Depends. Do males and females also use their ears for other purposes, such as detecting prey or predators?  Is hearing ability much greater in males than in females? Darwin specifically addresses such a scenario. (Last sentence of page 256, first part of page 257.)
I think these ideas play out for most of your scenarios. It depends on if the traits differ between the sexes (not specified in your scenarios) and the traits lead directly to increased male reproductive success. But I will address one more.

The males need good camouflage because when they fly to find a mate they may get eaten by a predator and die before reproducing. Here the difference is that the predators are attracted to the spot if they can sense many males. So the presence of the other males influence the probability of finding a mate of a given male. Is SS is involved in the adaptation to good flying abilities?

In this case, I would say not SS. The camoflage is necessary for survival, not direct reproductive success. This is natural selection.  Increasing the probability of finding a mate is not the same as guaranteed reproduction.


Specificity of the adaptive lymphocytes T cells are known for their ability to bind multiple antigens, owing to the degeneracy of the recognition sites on their receptors. [I] When examining the structure of the T cell receptor, we can observe the ɑ and β chains which have a highly variable region, in their extracellular domain:

From what I understand, TCR degeneracy means that one receptor can bind to different antigens.

In comparison, the B cell receptor consists of a recognition site that contains a membrane-bound isotope of immunoglobulin. Again, from what I gather, variation in both the Ig on B cells and the TCR occur as a result of genetic recombination. [II]

Question:

Does the membrane-bound Ig in the BCR exhibit the same degeneracy as TCRs? Does variation caused by V(D)J recombination work the same way for both these receptors?

References:

[I] https://en.wikipedia.org/wiki/T_cell_receptor

[II] https://en.wikipedia.org/wiki/V(D)J_recombination

[Images] http://what-when-how.com/acp-medicine/adaptive-immunity-antigens-antibodies-and-t-cell-and-b-cell-receptors-part-2/

This is incredibly oversimplified, but the short answer is that both T and B cells can have degenerate recognition, though the molecular mechanisms are somewhat different.

T cells recognize linear sequences of amino acids that have been excised from their parent proteins, from 8 to 16 or so amino acids long, and that are associated with MHC proteins.  The association with MHC proteins depends on the specific sequence of amino acids, and you can think of this association as depending on a number of amino acids (let's say 4 or 5) that point "down" into the MHC.  That leaves maybe 4-10 amino acids pointing "up" that can interact with the T cell receptor.  If you search for a random set of 4 amino acids with a given spacing, it's quite likely that it will turn up several times in a large protein database; even more often if you allow some degeneracy (similar amino acids can substitute sometimes).  Therefore, yes, T cells tend to have a moderate amount of degeneracy in their epitope recognition.  However, while search a whole database may find duplicates, the degeneracy is not terrible, and the MHC binding requirement also reduces it quite a bit. Also, of course, during T cell development, TcRs that have broad and degenerate recognition of many structures are selected against.  So T cells are definitely cross-reactive, and sometimes extensively so, but in single individuals it's probably not a common thing.  (Ray Welsh and Liisa Selin have looked at cross-recognition between viruses and find quite a bit of cross-reactivity, though, so this may be understated.)

Antibodies, unlike T cells, recognize conformational epitopes rather than linear sequences.  However, just as with linear epitopes, it's not impossible for two unrelated proteins to end up with similar conformations, even with rather different amino acids.  As well, antibodies can be more or less "forgiving" in their recognition; some are extremely specific, but others can interact with a wider range of shapes.  You can imagine a "flat" antibody binding surface that is rather generic, that could interact with many different shapes. Again, B cells with broad cross-recognition are selected against during development, though not as rigorously as are T cells.


How does a Coronavirus "test kit" work? A number of countries are using test kits for detecting new cases of nCoV (2019-Coronavirus) and apparently China is running low.

What exactly is in a nCoV "Test Kit" — How does it work?

(Surely they also differ, so in which way do they differ?)

The CDC has made available online its nCoV test kit. Briefly,the kit contains primers and probes for real-time reverse-transcriptase PCR, as well as instructions for appropriate use and (critically) controls and guidelines to avoid false positives and negatives. Kits from different countries may use slightly different primers and probes, though since they are all working from the same sequences and the same principles they should be broadly quite similar.

Explaining how quantitative PCR works and the details of the primers and probes is out of the scope of this SE. A layman's introduction was written by John Timmer at Ars Technica.


Are there any structures in mammals that are used only by males? There are examples of structures which only serve a purpose in females, but it seems like the opposite could also be true. Are there any structures which exist in both mammalian sexes and only serve a purpose in males?

Some researchers consider the neural circuitry responsible for orgasm vestigial in women. I disagree with this for a number of reasons, but here is a book exploring the hypothesis:

http://www.amazon.com/The-Case-Female-Orgasm-Evolution/dp/0674022467/ref=sr_1_1?ie=UTF8&qid=1336286206&sr=8-1


How many eukaryotes are there on Earth? I have been reading:

  William B. Whitman, David C. Coleman, and William J. Wiebe, "Prokaryotes: The unseen majority", Proc. Natl. Acad. Sci. USA 95, pp. 6578–6583, June 1998.  [Full Text] [PDF]

wherein they estimate the number of prokaryote cells on Earth to be of the order of $10^{31}$.

I can't seem to find any equivalent data for eukaryote one-celled life. Are there any estimates for the number of one-celled eukaryotic living things on Earth? Do any other estimates confirm or tell against the reference I have cited above?

Could not fit in a comment....

To make sure we all understand your question...

Is your question how many (eukaryote) species are currently living? or How many (eukaryote) cells are currently living??

Just a hint to answer the question

Micheal Lynch, in his book (On the Origin of Genome Architecture) at page 3, Box 1.1 tries to answer the question How much DNA is there on earth?. He ends up with an estimation of a total length of DNA on earth of $10^{24}$ km for procaryotes, $10^{25}$ km for eukaryote (of which $\frac{1}{1000}$% is accounted to humans). This sums up to a total DNA length of $10^{12}$ light-years, or 10 times the diameter of the known universe!

In his calculations, he estimates that the total number of procaryote cells at $10^{30}$ (citing Whitman et al. 1998 as you did). He estimates the total number of eukaryote species to $10^7$, i.e. 6 times the number of known eukaryote species. However, he doesn't directly give any reference for this estimate but he refers to different chapters in the book that contain lots of references.

...I hope that helps...


Why don't flies avoid the motorway? Flies have a short lifespan, therefore evolution should technically happen over a shorter period of time (years).

Flies die all the time from getting hit by cars on the motorway.

Those flies that don't go near the motorways have a greater chance of reproducing.

If this was an advantage (motorway avoidance = not dying), shouldn't more and more flies be avoiding the motorway?

Cars have been around since, roughly ~1950. That's 60 years.

Why don't flies avoid the motorway?

Flies can and do evolve quickly thanks to a short generational time. However, your question seems to stem from a misunderstanding of what evolution entails.

Evolution occurs when the genome mutates. Why it mutates isn't particularly relevant, but a gene (or genes) mutates and as a result of that mutation a characteristic of the organism changes. It doesn't have to be a big change. Maybe a single protein somewhere operates 2% less efficiently, giving practically no outward signs of evolution. Sometimes it can be big - changes in coloration, changes in sensory perception, lifespan, etc.

In order for mutations (beneficial or detrimental) to have a significant effect across an entire population, the population itself has to be fairly small or the mutation has to give a large advantage over the old version.

Flies are not avoiding motorways because a mutation that specifically codes "AVOID CARS" is going to be very unlikely given that it would you would first have to encode what a "CAR" is in order to avoid it. That probably won't happen because on the time scale that evolution usually acts over very large populations (which flies have) we won't be driving cars by the time necessary for deaths due to cars has a serious effect.

Flies have huge populations and breed extremely quickly, so even if a few million are killed by cars, it doesn't put a dent in their population numbers. There's no reason for the change to occur. Combined with the extreme difficulty of actually encoding a gene specific to cars, the odds are it just won't happen in any realistic time-frame.


Are there any primary structure sequences that strongly suggest b-sheet or alpha helix? Is there a particular sequence of amino acids that we know will take on a beta-sheet or an alpha helix or is it essentially random?

Yes, there are certain amino acid sequences that tend to form alpha-helices, and others that prefer to form beta-sheets. There is no perfect correspondence between sequence and structure, but there is a statistical relation where presence of certain amino acids in particular sequences makes one conformation or the other more likely. For example, alanine, glutamate, leucine and methionine tends to be present in alpha helices.

This topic has been studied for 50 years or so, and there are many methods available for predicting structural features from an amino acid sequence. See this list of available software, and this article about protein structure prediction in general.

See this table from another answer on this site which shows which individual amino acid prefers which secondary structure (higher value shows higher preference):