How is it known that Homo sapiens and Homo neanderthalensis interbred? Many recent articles maintain that a small percentages of Neanderthal genes (up to 2%) are found in modern non-African people. (I believe that currently there is insufficient genetic material from older hominids, such as H. erectus, to decode a genome).

My question is: how is it known the “Neanderthal genes” found in modern humans got there by way of interbreeding? What distinguishes those genes from genes that both species inherited from a common ancestor? After all, Neanderthals and H. Sapiens are over 99% genetically identical. How is it determined that gene A is found in both because it was from H. erectus, from which both evolved; but gene B was not already present in H. sapiens, so it must have arisen through interbreeding?

Although this question makes some false assumptions, it is fundamentally interesting as the methodology used is neither simple or easy to understand. It is not my area, but I have found it especially interesting to read the long 2010 Science paper by Green et al.. One really needs to read it for oneself (it is free view), but it is not a trivial undertaking.

False assumptions / misconceptions in the question

The main misconception in the question are:

That it is necessary to know anything about the genome of H. erectus to make these conclusions. The methods used do not require this. (Although comparison with chimpanzee is sometimes used to give an indication of whether a genetic change occured in humans or Neanderthals.)
That the similarities and differences under discussion relate to differences in complete genes — “but gene B was not already present in H. sapiens…”. They do not, which makes the analysis more complex to follow.

Towards an explanation

Let me start by addressing the question “What distinguishes those genes (purported to have been acquired by H. sapiens from Neanderthals) from genes that both species inherited from a common ancestor?”. The answer relates to the absence of such genes from modern humans of African origin, and the fact that we know the general evolutionary relationship between neanderthals and modern humans (African and non-African) from a wealth of non-sequence paleontological evidence. This is shown in the diagram below, modified from a recent and recommended review by Nielsen et al. in Nature (2017).

Clearly any gene present in the common ancestor to humans and Neanderthals should be present in both African and European populations, unless it had been lost from the African population.

So if the analysis is not done by detecting gain/loss of individual genes, how is it done? Certainly not by overall percentage sequence similarity, because of the high overall similarity and the population variation. It is done by studying SNPs — single nucleotide polymorphisms — in particular genes.

For example, consider a gene that has only a single haplotype in Neanderthals, and originally had a single but different haplotype in humans. (This might determine something like eye colour, although this is not an actual example.)  If the other haplotype were acquired by humans as a result of interbreeding, then the modern human population would contain both alleles. When you compared the relationship of the SNPs for this gene between different humans and between humans and Neanderthals you would find different results from those for a gene the variant of which had not been acquired by interbreeding. The acquired gene in humans would be more related to that in Neanderthals than non-acquired genes, but less related to that  in other humans (because of its more recent appearance in the population and time for homogenization, I believe).

The African/non-African aspect is explained in the Science paper cited in my introduction, but there is a good visual diagram in a 2014 Nature paper by Sankararaman et al., the manuscript of which can be viewed freely in PMC through the US HHS.

(1) Sites where a panel of sub-Saharan Africans carries the ancestral allele and where the sequenced Neanderthal and the test haplotype (marked non-African) carry the derived allele are likely to be derived from Neanderthal gene flow; (2) Haplotype divergence patterns. Genomic segments where the divergence of the test haplotype to the sequenced Neanderthal is low while the divergence to a panel of sub-Saharan Africans is high are likely to be introgressed.

These papers contain a wide range of controls, including comparisons of different non-African population groups, and detailed discussion of alternative possibilities.

A final point of interest is that Sankararaman et al. examined some of the genes in which these SNPS suggest Neanderthal origin. They write:

  “…genes involved in keratin filament formation and some other
  biological pathways are significantly enriched in Neanderthal
  ancestry in European populations, east-Asian populations, or both
  …. Thus,
  Neanderthal alleles that affect skin and hair may have helped modern
  humans to adapt to non-African environments.”

Coda

It would be scientifically dishonest not to mention some oddities. One is that the Green et al. paper suggested that gene flow had been uni-directional: from Neanderthals to humans, which is apparently unusual in interbreeding. However a more recent study (Kuhlwilm et al., 2016) shows some human gene flow into Eastern Neanderthals, although not into European Neanderthals. (Thanks to @iayork for pointing this out.). The other is that modern Asians appear to have more Neanderthal DNA than modern Europeans. (This is discussed in the paper already mentioned by Green et al.)


Can I image Coomassie and GFP in gels at the same time with a fluorescence scanner? I'm working with a GFP-tagged protein and am routinely using a fluorescence imager (GE Typhoon) and a standard optical scanner to capture fluorescent and absorption images, respectively, of my SDS-PAGE gels.  The Typhoon supports multiple channels, so is there some way that I can scan for the two on the same device (GFP + total protein)?  I assume I can't do absorption on a fluorescence scanner..

I could manually register the two images, but it would be laborious as they are at different resolutions, slightly different rotations, and the gel can stretch ever-so-slightly when placing it on the platens.

Coomassie blue fluoresces in infrared when bound to protein, so if your reader has the appropriate filter set, it should be possible.


Why is prothrombin time test not used for heparin Prothrombin time test is used for the monitoring of warfarin but not heparin. Why is this used for warfarin monitoring and why is it not used for heparin monitoring?

Thats because the mechanism of action is different between warfarin and heparin.
Warfarin inhibits the formation of prothrombin (also known as factor II) by inhibiting the metabolization of vitamin K (for extensive details have a look at the Wikipedia article about Warfarin).

Heparin inhibits the blood coagulation by binding to antithrombin III which functions as a inactivator of active clotting factors as factors V, IX, X, XI and XII. It also binds calcium which is important for the blood coagulation. For more details see the Wikipedia under Heparin.

Therefore Heparin interferes with the formation of Thrombin and the test does not work. A nice image of the coagulation cascade can be found here, which also shows the points where Heparin interferes. The test can be done with Batroxobin, see here.


Complexity in creating transgenic animals (e.g., mice) Many papers I have seen describing transgenic rodent models (and presumably applicable to other model organisms) involve the knock-in, or modification to, a single gene, possibly two genes. With respect to recombineering techniques, what prevents targeting multiple genes in a single organism? For instance, if I wanted to simultaneously knock-in some genes and knock-out others within the same mouse, would I be forced to generate individually modified transgenic lines and then do some "fancy" breeding to generate the multiple-modified mice?

One reason is the low likelihood of success. Modifying a gene almost always involves a recombination event of plasmid DNA with a target site in the genome (and I say almost just because there may be some method that I don't know about, but all the ones I'm familiar with do). The likelihood of that decreases exponentially with the number of genes you're trying to modify. If you're trying to make several mutants of individual genes the likelihood of success decreases only linearly.

Another reason is having more knowledge and experimental power. You can learn little from a double mutant if you don't also have the individual mutants to compare. In fact, most reviewers would ask for individual mutant data if you've made a double mutant in your paper. This is especially true with flies and worms, as crosses take less time with them.

Also, the more mutant genes you have, the weaker the animal. Your mutants may not be viable at all with too many mutations.


Are there any open plant databases (database/library/collection), containing species information and pictures? I would like to download a plant database containing photos and species details. Do you know if there are any openly available online?

Large online floras have the advantage of not only having details and often photographs and illustrations, but also being (more or less) definitive, that is, botanists will refer to them.

See my answer here for links to examples, and also for some of the problems with using floras (e.g. not easily downloadable).


Can a hairpin (stem loop) within a transcript stall a eukaryotic ribosome? Is their evidence of RNA secondary structure causing a stall in translation within a eukaryotic cell?

Can a hairpin (stem loop) within a transcript stall a eukaryotic ribosome?

It seems that could happen.
C9orf72 translation is one of the examples. In this gene, GGGGCC repeats exist in 5' UTR of the mRNA (upstream of the first ATG). The repeats expand in subsets of neurodegenerative disorder such as ALS. The repeats can form a stem loop structure and stem loops of expanded repeats are more stable.

mRNAs having expanded repeats seems producing poly-GlyAla, poly-GlyPro, and poly-GlyArg peptides which codons are GGG-GCC, GGG-CCG, and GGC-CGG from different frames from GGGCC repeat.

This means the translation starts somewhere in or upstream of the repeat without ATG. To explain this, there is speculation that ribosomes stall because of the tight structure of the stem loop by expanded GGGGCC repeats, mistakenly take tRNAs and start translation. It is called "Repeat-associated non-ATG translation".

You might want to refer to:
Repeat-associated non-AUG translation and its impact in neurodegenerative disease.
https://sites.tufts.edu/als/the-answer/c9orf72/
RAN translation and frameshifting as translational challenges at simple repeats of human neurodegenerative disorders


How do I offer a generous gift to sweet-seeking wasps, bees, hornets, bumble-bees? I was having ice coffee and melon ice and after visiting the lavatory I saw that a wasp was having a good time with my already finished ice coffee.

Trying to begin the melon ice the wasp kindly insisted to take a first bite despite my insistence to not do that.
Feeling generous, I offered the wasp the already accepted ice coffee, but despite my best efforts (Waving it in the correct direction so that it get the smell directly before its nose) it only flew uselessly in circles.

Is there any method to give those sweet-seekers a meal which they gratiously accept (and in effect save us the nuisance to shoo them away) ?

There are many scientific methods for that which are widely used in animal behavior studies, specifically in honey bees. Read this this. If you search you can find similar for mice and rats also :P


Human Anatomy and Physiology - The Muscoskeletal System In the human limb skeleton can you identify a bone which is rather feeble and does not have much role in supporting body weight or maintain posture, and doctors use pieces of it to transplant to other broken bones, where necessary?

For bone grafts, they usually use parts of the bones, so their removal should not result in problems with the "body weight maintenance" or "posture."

Parts of the fibula (calf bone) can be used, for example, as a graft to repair avascular necrosis of the femoral neck or congenital pseudoarthrosis of the tibia (shinbone) (International Orthopaedics).

For spinal fusion (joining the vertebra in the spine), they typically use the bone from the iliac crest (the top part of the pelvis) (OrthoInfo).

Other bones that can be used as grafts:

Parts of the ribs and certain skull bones for reconstruction of the facial bones
Parts of the mandible for tooth implants
Upper part of the tibia for various purposes
Distal part of the ulna for correction of the wrist in rheumatoid arthritis


How do you read the histone code? I took it upon myself to research how methylation/acetylation affects histone tails via post-translational modifications. However, I find myself confused about how to "read" this histone code, specifically for the Euchromatin.

My problem is that there are both acetylations and methylations. Does that mean that the methylation of lysine 4 will cause that portion of the chromatin to be condensed, but the acetylation of the lysine 9 and so on will cause that portion to be decondensed?

The "histone code" is not like the genetic code where one codon in an ORF always is translated to a single amino acid. It's closer to something like GC content or CpG islands: a single instance doesn't tell you anything, but enrichment over some finite window may be biologically significant.

You may want to review the basics, starting with the Wikipedia page on the histone code. In particular read the paragraphs at the end:

  Every nucleosome in a cell can therefore have a different set of
  modifications, raising the question of whether common patterns of
  histone modifications exist. A recent study of about 40 histone
  modifications across human gene promoters found over 4000 different
  combinations used, over 3000 occurring at only a single promoter.
  However, patterns were discovered including a set of 17 histone
  modifications that are present together at over 3000 genes.[13]
  Therefore, patterns of histone modifications do occur but they are
  very intricate, and we currently have detailed biochemical
  understanding of the importance of a relatively small number of
  modifications.


how does a dna probe work in DNA fingerprinting? It says in my textbook ' after hybridisation with VNTR probe,  the autoradiogram gives many bands of different sizes '.  I tried looking on the net and it said there that probe is ' a radioactively labeled ssdna which binds to complementary dna '
My question is,  how do we know that if the DNA we are testing does contain complementary sequences?

You should look up VNTR. Take a look at the wiki page and it will tell you that VNTRs are Variable Number Tandem Repeats, the length of which varies between individuals, making these irreplaceable in DNA fingerprinting and such.

The trick is, all individuals will have it, but the pattern will be different, so you probe such regions which are formed as a stretch of k-mers. And you already know that they will be complementary, because we all carry them.


Are Sciomyzidae fit to combat snails? I read that Sciomyzidae are also called snail-killing flies, which immediateley made me think: "I need those"!

Questions:

Are they really fit to control snail over-population in my garden? and
if so where do i get them?

Short answers:

These insects live near water or marsh areas so that's where you can get them from. This is because many species of this group has larvae that are aquatic or semi-aquatic.  According to wikipedia:

  The adults drink dew and nectar.

And it is their larvae that either prey on or become parasites of gastropods.

In this article the following is stated:

  (...) Sciomyzidae is of interest from practical viewpoints because of their potential as biocontrol agents of aquatic snails carrying diseases (e.g. schistosomiasis and fascioliasis) and terrestrial, pestiferous snails..

So the answer is yes, they might be fit to use as biological pest control, yet they may not be suitable against all species. Details of their life cycle and their biology can be found in the linked article or in this book:
https://books.google.hu/books?id=vqE1AMIj-HUC&pg=PR16&lpg=PR16&dq=Sciomyzidae&source=bl&ots=pCVJJUu2cb&sig=M1F8GhR51VI1Y62htF7eX0kNpfo&hl=hu&sa=X&ei=AF0uVf_tKI3taNLhgIAL&ved=0CFgQ6AEwBzgK#v=onepage&q=Sciomyzidae&f=false


Which species of bumblebee(?) is this? I observed this beautiful insect near a forest in northern Switzerland. What is it?

To me that looks like a "hover fly" — specifically the Pellucid Fly (Volucella pellucens).

Compare with:

This species is present throughout Europe according to the wikipedia article (first link).


Transposons and the net amount of DNA The retrotransposons and certain DNA-transposons, are "jumping" sequences which may be incorporated elsewhere in the genomic DNA of an organism, through varying mechanisms. This insertion is almost random in case of retrotransposons and most DNA-transposons, but some transposing enzymes show specificity in selection of insertion sites. In either case, the "copy-paste" mechanism of transposition is essentially a random process(considering the frequency and place of transposition) and therefore, the extent of transposition should vary among all individuals, and all cells of a single individual. My question is,

  Is the extent of transposition random and varied among the different
  somatic cells of an individual or is there a regulatory mechanism which ensures that
  there is not much difference in the net content of DNA (caused by unequal transposition) by equalizing
  the extent of transposition in different individuals or different
  cells of the same individual? If not, does this unequal c-value in different cell cause any troubles?

Transposition may occur at any given time in life, and in any cell. There are several cases known where transposition interests somatic cells (give a look here for reference). However, the frequency of transposition events is low, and the difference in amount of DNA between different cells in an individual is low. When you reason at the level of different individuals, however, the proportion of genome affected by transposable elements may be relatively high (give a look here for a reference)


Why do telomere lengths not predict differences in life spans among species? We read that ageing is related to cell death when we run out of telomeres at the end of our DNA molecules. Humans live roughly for 70 years - the traditional three-score years and ten. This compares with the great apes, such as chimps and gorillas, which live for about 40 years. So we would expect the great apes to have fewer telomeres than humans. In fact the reverse is the case. Humans have telomeres of about 10 kilobases in length whereas the equivalent length in chimps and other great apes is about 23 kilobases. So what is going on? Why do we live longer?

The answer should be obvious: Telomeres do not determine an organism's longevity.

There's only a vague correlation between telomere length and a species' lifespan.  See Comparative biology of mammalian telomeres: hypotheses on ancestral states and the roles of telomeres in longevity determination for a starting point.  Telomeres are a part of the longevity story, but probably a fairly small part.

The Hayflick limit is generally associated with telomere length. Human telomeres are a little on the long side as species go, but are not extraordinary. Many species of mice, and other rodents, have far longer telomeres than humans, for example, and obviously have much shorter lifespans. There's also such a thing as a "mega-telomere", found in a number of bird species, which can hundreds of times longer than human telomeres.


Is it possible to train allergic resistance by exposing yourself to allergens? My hypothesis is that one can decrease the allergic reactions over time by continuously exposing yourself to slowly increasing doses of allergens.

Is there any scientific evidence pointing this right or wrong?

The phenomenon called oral tolerance is quite a common way to reduce allergic reactions. Basically patients have to eat a lot of the antigen with their daily diet under the supervision of doctors, so in time allergic reactions can be alleviated. The idea behind this is that our immune system is much more tolerant to things that get in our digestive system (in most cases). Here is a good article on oral tolerance from Nature.

Citation: Pabst, O; Mowat, A M - Oral tolerance to food protein Mucosal Immunology 2012 https://doi.org/10.1038/mi.2012.4


How do organelles divide? I'm sure by the nature of this question you will come to know my amateurish knowledge in biology. During mitosis, they simply state that the organelles just replicate...while we are provided somewhat detailed information regarding the division of the cell. How do the nucleus and the other organelles divide? Mitochondria used to be prokaryotes apparently so do they divide by binary fission? while we're on that what exactly are the organelles composed of? There is a spike in protein production during interphase...so how do the organelles even go about dividing?

Well, the nucleus does not divide per se. Remember, the nuclear membrane dissolves during mitosis. It starts reforming after metaphase. Here is a review detailing the process and the mechanisms which are known. By extension, the Endoplasmic reticulum gets portioned as it is derived from the nuclear membrane.
Organelles also rely on the cytoskeleton and associated motor proteins for distribution between the daughters. A debated aspect in this regard is whether the organelles are distributed at random or is there an active process that ensures similar distribution between the daughters.
Finally, on to mitochondria. Till this point we have assumed symmetric cell division i.e. both daughters get almost equal amounts of maternal material. But in stem cell divisions, the non-stem daughter is smaller in size. Interestingly, this paper shows that the stem like daughter gets younger mitochondria (less damaged mitochondrial DNA).
As you can see, it is impossible to cover all the organelles in a single answer. And we are not even considering physiological differences between different cell types. Cheers!


How much of human's behaviors and preference can be explained by evolution? I'm talking about things like the tendency to feel sleepy after eating, avoidance of excrements, general preference for sweet foods, etc. Do all those characteristics have biological or evolutionary basis?

What is heritability?

First of, please read about the concept of heritability. See for example the post Why is a heritability coefficient not an index of how “genetic” something is? You should be able to understand why all else being equal, why if environmental variance for a given phenotype increase it results in a decrease in heritability and why directional selection in a population decreases heritability.

Do you now know what heritability is and is not?... Good!

Your question is very broad...

As you now understand, heritability is a concept define for a given population in a given environment and most importantly for a given trait. There is no way to give a single answer for all traits one might want to consider.

By experience, it seems that, in humans, most behavioural traits that we decided to investigate has heritability estimates in the order of 0.05 - 0.6.

One example

I will consider just one of the trait you list, "preference for sweet foods". Sweet taste preferences appears to have a high heritability in humans with estimates of the order of 0.41-0.66 (Keskitalo et al., 2007). For heritablities about other food preferences, you might want to have a look at Reed et al. (1997; there are probably more recent papers that make better reviews though).

Preference for sweet foods


What kind of flower is this? I was in my garden a few days ago and found the flower shown in the pictures.
Can anybody tell me what this flower is?

Location: Germany / northrhine westfalia
Date: February 2017
Season: Winter

[Edit]:
My neighbour thinks it is a Anemone hupehensis (en.wikipedia.org/wiki/Anemone_hupehensis), could be right.

I think it is Anemone hupehensis. We have this species in our garden, and the seeds and dead leaves look very similar to the ones in your picture. The leaves are large,jagged and palmate and they have beautiful flowers in the summer/autumn (I've seen red, pink and white). The fruits/seeds also look very distinctive and cotton-like. The species is originally from Asia/China.

Here is a picture of the fruits/seeds:

(Hard to find good ones, this from Instagram page http://www.ipopam.com/tag/höstanemoner)


In what sense is the "histone code" a code? Since I started learning about molecular cell biology, I have witnessed an increasing amount of attention to this thing called a "histone code." However, unlike the central dogma of molecular cell biology (i.e. DNA RNA Protein), I still feel very confused about what exactly constitutes the histone code. Is this term code being used rigorously like it is for the central dogma? That is,  is there an actual code? If so, what is its alphabet (e.g. GTAC for DNA, GUAC for RNA, the amino acids for  proteins)? What kind of words does it encode (e.g. codons for RNA to protein)?

If these things are not known, how do we know it's actually a code then?

Thanks!

As already mentioned by Stefan, the "histone" code is not really a universal code; it is restricted to eukaryotic systems and even then, not unambiguous. It is, at present related to two kinds of histone modifications and their correlation with the transcriptional activity at that locus:

Methylation
Acetylation

Other modifications such as phosphorylation and ubiquitylation also exist but they are not generally considered in this "code".

Acetylation masks the histone's positive charge and thereby loosens the chromatin (DNA wrapped around the histones), which in turn facilitates transcription. Therefore acetylation is almost always activating in the sense of gene expression.

Methylation, on the other hand has different effects. Methylation on Histone-3 at 4th lysine (H3K4) and H3K36 causes activation whereas H3K9 and H3K27 are repressive. There is also some difference between different extent of methylation i.e monomethylation, dimethylation and trimethylation. The effect of methylation is executed by proteins that have domains such as chromodomain and PHD fingers, that identify these modified histones. Sometimes the histone can carry both kinds of methylation marks H3K4me3 and H3K27me3 and these are called bivalents.

Other histones of the octameric nucleosome can also be modified. However as with other kinds of modifications that I mentioned previously they do not seem to be very common and are therefore not generally considered in this "code".


Pharmacokinetics: why do certain drugs follow zero-order kinetics? I understand that alcohol and phenytoin are two examples of drugs that follow zero-order kinetics. Why do these two particular drugs follow zero-order kinetics as opposed to first-order kinetics?

Basically any compound in concentrations sufficient to saturate its metabolization machinery will show zero-order pharmacokinetics. This reflects the fact that metabolization is taking place at full speed while facing a comparatively enormous amount of substrate (just as @WYSIWYG pointed out). This effect can also be shown in vitro with pure substrate/enzyme solutions.

But the above is a rather simplistic model, valid only in specific situations.

Most of the time in humans, zero-order kinetics stem from the fact that liver enzymes are saturated. However, for most drugs the redistribution phase is much more important than metabolization/elimination in defining the duration of effect. A good example of that would be sodium thiopental. As a single iv bolus dose, it will induce loss of consciousness for a short time due to redistribution. However, continued infusion will allow blood and tissue concentrations to equilibrate, and then the metabolization/elimination rate will become much more prominent in defining the duration of effect. And as sodium thiopental happens to have zero-order metabolization kinetics in continued infusion, it will take you a loooooooooong time to wake up! This is why in human pharmacology, we use context sensitive half-life to better represent drug kinetics.


Is there any way a human could whistle and be unable to speak? Is there any situation anatomically, where a human could understand the speech of others perfectly, without any capabilities of speech themselves, but would retain the ability to whistle with a tune?

I was led to believe that the larynx is the most important thing for creating the sounds in speech, however I don't know if a damaged larynx would necessarily not allow someone to speak.

I would suggest someone who has no tongue cannot speak coherently, however I would imagine that the tongue is instrumental (pardon the pun) in creating a range of sounds whilst whistling.

Is there perhaps a part of the brain that could be affected in order to stop someone speaking? Or would this also mean the person could not understand speech either?

Short answer(s)
Someone with a damaged larynx may still speak with the use of a speech aid (electronic larynx).

The ability to understand speech does not necessarily mean one can speak normally. There are neurological disorders where folks can understand speech, but have difficulty producing it.

Background
A full removal of the larynx (laryngectomy) prevents the patient to produce speech because the vocal chords are removed. However, with the use of a voice prosthesis this can be solved (Cancer Research UK).

There are neurological disorders where one can still understand speech, but has impaired ability to generate it, called apraxia. Apraxia can be acquired or congenital (developmental) (NIH). The developmental type is not well understood a the neural level (Dyspraxia Foundation UK). The acquired type is known to occur through damage to specific brain areas, for example due to trauma or stroke. One of these areas associated with acquired apraxia is Broca's area (Graff-Radford et al., 2014), which is a brain area intimately associated with the production of speech .

Broca's area. Source: UC Irvine

However, although damage to this area can result in pure apraxia (i.e., impaired speech but normal speech understanding), it can also result in Broca's aphasia, which means that language understanding is also impaired (American Heart Association). Moreover, regarding your specific question, apraxia is characterized by impaired speech, but not a total lack of speech production.

Reference
Graff-Radford et al. Brain & Language 2014;129:43–6


What does ensemble-based model of enzyme mean? I am reading Pan et al. (2000), a paper about dihydrofolate reductase (DHFR).  They claim using a ensemble-based model of DHFR.

What is a ensemble-based model?

An 'ensemble' is a set of related models of a structure.

For example, conformational ensembles describe the structure of flexible proteins. There is a database of such structures here : http://pedb.vib.be/.

When NMR is used to determine a structure, the result is an ensemble of structures (see this paper for a comparison with crystallography). However, it is possible to see multiple structures for crystallography as well. This paper on "Accessing protein conformational ensembles using room-temperature X-ray crystallography" describes limitations to the idea of crystal structures having one unique structure.


If I squash an insect and it produces red "juice", does it always mean it is a blood-sucking type? If I squash an insect and it produces red "juice", does it always mean it is a blood-sucking type of insect? Or do some insects have red "juice" themselves, so the color is red on its own and not caused by sucking higher animal's blood?

I squashed a small fly-like insect recently, it produced a red stain, so I am wondering if the stain come from the insect itself or if it has to be some other animal's blood.

No - invertebrates don't have "blood" though they do have hemolymph. Hemolymph flows around the body cavity, rather than through vessels such as veins and capillaries, and comes in to direct contact with tissues and generally it is not red.

Hemolymph fills all of the interior (the hemocoel) of the animal's
body and surrounds all cells. It contains hemocyanin, a copper-based
protein that turns blue in color when oxygenated, instead of the
iron-based hemoglobin in red blood cells found in vertebrates, thus
giving hemolymph a blue-green color rather than the red color of
vertebrate blood. When not oxygenated, hemolymph quickly loses its
color and appears grey. The hemolymph of lower arthropods, including
most insects, is not used for oxygen transport because these animals
respirate directly from their body surfaces (internal and external) to
air, but it does contain nutrients such as proteins and sugars.
~ http://en.wikipedia.org/wiki/Hemolymph

The red you see from squashing, depending on the insect, could come from blood of other animals or (eye) pigments produced by the insect. For example, in my lab we have some Drosophila melanogaster with red eyes and some with white eyes (they carry a genetic mutation which represses the production of pigments in the eye) - if I squash the red eyed fly red "juice" is left on the desk, this doesn't happen with the white eyed flies.


Where do all the NAD+s come from? In the mitochondrial respiration (of plant cells) NADH is reduced from Nad+ as part of the TCA (converting malate to oxaleoacetate).

But where do the NAD+s come from?
The TCA cycle is working even in isolated mitochondrias by adding malate as a substrate, which indicates NAD+ must be present already.

I am also wondering if ADP and NAD+ can be transfered through the inner membranes of the mitochondrion without specific channels?

There is of course a pathway that synthesizes NAD+ de novo, usually from tryptophan, aspartic acid  or vitamin B3, or salvaged from compounds like nicotinic acid, nicotinamide. You can read more about it here: https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide#De_novo_production
The fact that TCA works in isolated mitochondria is not necessarily the effect of de novo synthesis. The reason for that is the cycle-like fashion of NADH production in the TCA and consumption of that NADH for electron-chain reactions (which recreate NAD+) or other reactions involving oxidoreductases. Redox reactions do not change the overall amount of the coenzyme. But in a living cell, some reactions will irreversibly consume NAD+, ADP-rybosylation may be an example. Still, the cell prefers the salvage pathway over amino acid pathway, because it consumes way less energy.
ADP and NAD+ cannot pass through the membranes without channels. Both are polar molecules and only non-polar molecules such as steroids can freely pass through the cellular membrane without any help from transport proteins.


How can humans hear low frequency sounds using the cochlea which is tiny compared to wavelength? Humans can reportedly hear sounds as low as 31 Hz. If we consider the speed of sound in air to be 1125 feet per second, then a sound at 31 Hz will have a wavelength of about 36 feet.

Normally, to capture a sound or other wave, we need an antenna that is at least as long as the wavelength of the signal we are attempting to receive.

But with the ear this is plainly not possible. If the cochlea of a human ear were to be unrolled, it would have a length of about 1 inch. Thus, in the sense of being an "antenna" it would seem to be far too short to be able to receive a 31 Hz signal, yet somehow it does.

How does the ear sense such low frequency sounds?

You are thinking of antennas for EM signals such as the dipole antenna. In this type of antenna, an external field (EM waves) excite the antenna (creating an electric current) which you then measure. There is thus something like a transduction step, which is more efficient if you can use the spatial scale of the wavelength.

In the case of hearing sound waves, the ear does not transduce the mechanical signal into another modality, but is directly modulated by the hair cells.


Question about *Cryptosporidium hominis* Cryptosporidium muris infects mostly rodents and it is usually found in gastric gladns. Cryptosporidium parvum infects humans and certain animals and it is found in the terminal ileum and colon.

There is also Cryptosporidium hominis that infects only humans. My question is

  where exactly in the human gastrointestinal tract it resides?

This page seems to indicate that it adheres to the epithelium of different internal organs. They write:

The sporozoites are released and parasitize epithelial cells (b, c) of the gastrointestinal tract or other tissues such as the respiratory tract.

Here is the figure from that page:


What evidence is there on the medical effects of circumcision? If this is the wrong place to post this question, then I will delete it and post it were it belongs.

I have heard many conflicting things about circumcision.  I have heard that it reduces the rate of STDs, including AIDS, and cancer in the man and his wife.  On the other hand, I have also heard that circumcising babies can cause psychological harm and increases the rate of urinary tract infections.  Are there any reliable studies on this issue and what do the conclude?

Thank you for any and all answers.

This question has already been answered over at the Skeptics site in great detail.

See Does circumcision reduce HIV risk? and Does circumcision lead to a net increase in quality of life?. The answers are well-sourced and there are answers addressing both sides of the issue.


Local BLAST Copy Number per Hit I generated a series of local BLAST databases using makeblastdb of metagenomic data and am searching for the presence of a particular gene. While I can do the normal BLAST analysis looking at e-values, % identity, etc. I haven't been able to figure out how to determine how many times a given sequence exists in the database.

So: given a BLAST database of metagenomic data where a particular gene may exist multiple times, how do I determine the copy number of a given BLAST hit?

Thanks in advance.

Define a "Hit" (based on some cutoff- evalue, score etc)
Get output in the tabular format
Count number of hits per query — it is usually given in the header; if you want to look for some selected hits (based on some cutoff, then you can parse the file and find out)

Example file (header):

# BLASTN 2.2.27+
# Query: TCONS_00036712 gene=XLOC_017996
# Database: ../nt_db/nt
# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 1014 hits found

If you want to parse the header to look for number of hits then you can run this command in the terminal (if you have awk — there by default in linux and other unix based systems. For windows install gnuwin32).

awk -v OFS="\t" '/^# Query/{q=$3 FS $4} /^# .* hits found/{h[q]=$2} END{for(i in h){print i,h[i]}}' blastoutput.txt

To get the number of hits for a given criterion (for e.g. I just defined bitscore [12th column] to be >400)

awk -F "\t" '!/^#/ && $12>400{a[$1]++} END{for(i in a){print i,a[i]}}' blastoutput.txt


What is the meaning of "The Molecular Basis of Disease" What is the exact meaning of The Molecular Basis of Disease? I have one assignment which involves presenting Molecular Basis of a Disease. I am not really sure what points to add.

There is an ELSEVIER research journal by the name of BBA Molecular Basis of Disease (link to journal). I think their synopsis of what the journal is about will illuminate what is meant by The Molecular Basis of Disease.

  BBA Molecular Basis of Disease addresses the biochemistry and
  molecular genetics of disease processes and models of human disease.
  This journal covers aspects of aging, cancer, metabolic-,
  neurological-, and immunological-based disease. Manuscripts focused on
  using animal models to elucidate biochemical and mechanistic insight
  in each of these conditions, are particularly encouraged.

The keywords here are biochemistry and molecular genetics, so I would think of what kind of mutations, at what chromosomal locations can cause genetic disorders for example. Or in terms of biochemistry, what kind of biochemical environment can lead to alcoholic liver disease etc.


Are non-lytic viruses reproducing themselves in the host cell? Non lytic viruses can cause cancers like the HPV. But aren't they reproducing themselves as they don't ruptures the cell. Or are they just not reproduced in enough numbers so that the cell keeps working. But if they stays in the cell and/or not reproducing how are other cells infected to cause a tumor? Just by normal division or within a stem cell?

You are conflating production of infective viral particles with lysis of the host cell. While true for some well-characterized bacterial viruses, like lambda, or T4, there are other bacterial viruses that can produce infective particles without lysing their host cell (e.g., M13, and related viruses).

Likewise, in mammalian cells there are plenty of examples where either an RNA virus (like the RNA-tumour viruses, also called retroviruses) where the viral genome integrates into the host genome, but can also produce infective viral particles. These viruses have external coats that include both proteins and lipid bilayer membranes (the viruses pinch-off, or bud, from the host cells' surface).

Many DNA viruses also integrate a copy of their genome into the host cells' genome following infection (e.g., Epstein-Barr Virus (it can cause mononucleosis), and members of the Herpes Simplex virus family that infect neurons and can cause chicken pox, or genital herpes).  Once you are infected with these DNA viruses your body is never rid of them, rather your immune system and cellular defence mechanisms "fight" the infection such that the titre of infectious viruses drops to nil, but you still have a reservoir of circulating antibodies that can be detected--and used if you are exposed again.


What mechanism suppresses melatonin release in humans? I'm looking at melanopsin, a photo pigment in the human eye. One of its actions is to trigger suprachiasmatic nuclei SCN to suppress melatonin release. I'm interested in learning what is the exact mechanism that actually suppresses melatonin release. Is it another hormone or some way of modulating the pineal gland function?

Take a look at this (especially page 938): Coordination of circadian timing in mammals by Steven M. Reppert & David R. Weaver Nature 418, 935-941 (29 August 2002) | doi:10.1038/nature00965

  Sodium-dependent action potentials provide the primary means by which
  the SCN transmit circadian outputs to other brain areas and are
  essential to its role as a pacemaker1.

  Signalling molecules from SCN efferents include neurotransmit- ters
  and secreted factors. An output role for secreted factors comes from
  the results of SCN transplant studies that suggest that the
  alternating activity of SCN-derived ‘inhibitory’ and ‘activating’
  factors drives locomotor activity rhythms (and hence rest/activity and
  sleep/wake cycles) in rodents

There was also a mention of per/cry gene expression.


What is the scientific name of this butterfly? I have this  butterfly but I don't know its scientific name. I think that it's a common butterfly which can be seen everywhere (btw, I'm in Taiwan.) Thanks for your help :D

With the information given, I have to say I think it's a Spangle, Papilio protenor, of the swallowtail family, probably a male.

It also is listed on the butterflies of Taiwan.

See pictures for comparison:

........................Male...............................................female............................................................................


How does core-conductor model correspond to an actual neuron? Hi guys, looking at your average neuron, it is very difficult for me to imagine how this could be translated into a core-conductor model

On the neuron above, where would be the intracellular space and where would be the extracellular space? Also, where is this membrane we are talking about?

What may be confusing is that the myelin is wrapped around the membrane of the axon.

The easiest way to see this is in cross-section:

From here.

The axon is indicated by #1 in the diagram and the myelin sheath is #4

The intracellular space (as represented by the horizontal resistors in the case of your model of the axon) is the fluid, replete with ions, that is contained within the membrane of the axons.

At the nodes of Ranvier, there is a break in the myelin sheath, exposing the underlying membrane of the axon.  In membrane in those gaps of the sheath, there are sodium channels (voltage gated) and potassium channels that facilitate the influx and efflux of ions that "refresh" the action potential as it travels down the axon.  The extracellular space is simply the milieu of fluid in the space between the axon and any adjoining cells.  For the purposes of analyzing the currents of the neuron, the sodium and potassium ions (and the conductances of the channels) are all that you really need to be concerned with.

What is confusing about your diagram is that it represents the conductance -- the inverse of the resistance of the channels -- of the channels (inwards and outwards) as a single vertical resistor in between the horizontal resistors of the intracellular membrane. This oversimplification is handy when doing the cable theory-type analysis, but it betrays the actual physiology of the neuron.

From a model standpoint, I'm breaking all the rules here, but you can think of things like this:

where one "rung" of your resistor ladder has $r_m$ broken out into the 2 components and drawn differently.


Do any RNAs directly inhibit transcription In eukaryotes, microRNAs and small interfering RNAs, as part of protein complexes, can attack specific messenger RNAs with complementary sequences, thereby inhibiting translation. However, RNA can also complement DNA. So, do any regulatory RNAs directly bind to DNA (with a protein complex or alone)?

I am only interested in regulation, not modifying DNA (like CRISPR does). I assume that means I am asking if any regulatory RNAs persistently bind to DNA, blocking RNA polymerases?

This question is for either or both eukaryote and prokaryotes.

Yes there are reports of RNA directly inhibiting transcription.

RNA induced transcriptional silencing (RITS) is a well known pathway in Schizosaccharomyces pombe (fission yeast). Initial heterochromatinization is dependent on the RNA (as a DNA identfication module) that guides other functional proteins to the target (Also see Djupedal et al., 2009).

piRNA in higher eukaryotes are known to cause methylation of target DNA regions and thereby the repression of genes at these loci (Aravin and Bourc'his, 2008).

Some classes of small RNAs in C.elegans (such as 22G RNA) are also known to cause transcriptional silencing.

Many lncRNAs are known to inhibit transcription of their target genes. The most famous example would be that of XIST which causes epigenetic silencing of one of the X-chromosomes in the female.

On a purely biochemical note, RNAs can also form triplex with target DNA regions and impede transcription and replication (Bacolla et al., 2015).


What restriction enzyme was used in cutting this DNA piece? So, i was given this cut piece of dna and i was required to choose the restriction enzyme used to cut it. I had to pick either XhoI(CTCGAG) or TaqI(TCGA), where the sequence between parentheses is their palindrome sequence. Which one is it and why? I've picked XhoI since i know that the enzyme cuts in between the palindrome

GAGCT        C
C        TCGAG

DNA after the cut.

In order to keep this on topic, I will try and give a more general answer.

The most widely used restriction enzymes, and the ones typically taught first, all cut within their recognition sequences, however, this is not necessarily so as most Type I and Type III enzymes cut at a distance from their site, sometimes this is a fixed distance, sometimes it is not. It is only Type II enzymes that cut symmetrically within their sites, and even then, not all of them. However, cutting within the site is usually the most useful kind of cut for molecular genetics and thus these are the most common enzymes to encounter in the lab (see here for more).

For a particular enzyme, the best way to find the cut site is simply to google it or search directly on the NEB site (where you will likely find the top Google hit anyway), doing this for XhoI would get you a page containing information like this:

Where the little arrows in the given recognition sequence indicate where each strand will be cut, whereas as for enzymes that cut outside the recognition site you will get something like this (for AlwI) where the $(N)_4$ part tells you that the enzyme cuts four bases away on the 5'-3' strand, and the $(N)_5$ part tells you it cuts one base further away on the opposite strand.

In order to identify which of a number of enzymes cut a certain sequence you need only find the appropriate information for the relevant enzymes so you can compare these cut diagrams for the relevant enzymes.


Does direction relative to origin of replication matter on small plasmids? The recent question about forward vs. reverse strand got me thinking about directionality conventions in synthetic biology.
As noted in the answer to that question, if we consider only DNA in isolation, the strands are symmetric and there is no reason to prefer one over the other. A great deal of work in synthetic biology, however, is done on small plasmids, and there is definitely a directional context for these systems: the origin of replication.
The origin of replication is typically separated from the insertion point in an engineered vector, but the replication process is directional and goes around the whole plasmid. I am thus thinking that there may in fact be a difference in behavior caused by the interaction of transcriptional activity and the replication process, especially for a high-copy plasmid, where replication is much more highly active.
Does anybody know if this is, indeed the case, and to what degree is it worth being concerned about?

I like this question, and I had a similar thought when reading that "Forward or Reverse Strand" post. I've since found a 2005 publication by Mirkin and Mirkin1, which investigates the interaction between the replication fork and transcription machinery in context of an E. coli plasmid.
An excerpt from the abstract:

Studying Escherichia coli plasmids, which carry constitutive or inducible promoters in different orientations relative to the replication origin, we show that the mutual orientation of the two processes determines their mode of interaction. Replication elongation appears not to be affected by transcription proceeding in the codirectional orientation. Head-on transcription, by contrast, leads to severe inhibition of the replication fork progression.

To break this down, replication in E. coli proceeds at approximately 20 times the rate of transcription.2,3 From this, there are two kinds of collisions possible: (1) a "head-on" collision where replication and transcription complexes proceeding in different directions meet, or (2) a "co-directional" collision where the faster replication complex catches up to the slower transcription complex proceeding in the same direction.  Mirkin and Mirkin find that co-directional collisions have little effect on the procession of the DNA polymerase III holoenzyme, whereas head-on collisions
cause replication to stall.

One can clearly see that when transcription from the P7 promoter is codirectional with replication, replication was not affected (Fig.3A). Head-on transcription, in contrast, imposed severe constraints on the replication fork progression (Fig.3B).

Altogether, it is a gem of a paper, and I suggest reading the full discussion to best understand the limitations of their experiments and their caveats in interpreting the results. (e.g. the different rates of procession of DNA Pol I and III, and the frequency of polymerase switching.)

References

Mirkin EV, Mirkin SM. Mechanisms of transcription-replication collisions in bacteria. Mol Cell Biol. 2005 Feb;25(3):888-95.
Gotta SL, Miller OL Jr, French SL. rRNA transcription rate in Escherichia coli. J Bacteriol. 1991 Oct;173(20):6647-9.
Hirose S, Hiraga S, Okazaki T. Initiation site of deoxyribonucleotide polymerization at the replication origin of the Escherichia coli chromosome. Mol Gen Genet. 1983;189(3):422-31.


Exocytosis of mast cell secretory granules I've been doing a bit of reading about mast cell degranulation and have become thoroughly lost while trying to understand how the secretory granules are actually secreted.

I understand that there are many ways in which mast cells can be stimulated to degranulate, but I have been focusing on the example of IgE bound to FcεRI receptors. I believe I'm right in saying that antigen binding causes cross-linking of FcεRI receptors (since the antigen epitopes bind with the IgE paratopes and the IgE antibodies are themselves bound to the FcεRI receptors.) This recruits Lyn which phosphorylates ITAM motifs on the β and γ chains of the FcεRI receptors. This recruits Syk which is phosphorylated and activates LAT. This phosphorylates PLCγ which catalyzes the breakdown of PIP2 into IP3 and DAG.

All of this leads to the activation of PKC. I understand that PKC is (at least in part) responsible for the exoctyosis of SG but my question is by what means? Wikipedia, KEGG and this handy resource are all very cursory, whereas the academic papers which google turns up are way over my head.

So, if I might, what is it that PKC does and, in general, how are the secretory granules transferred from within the cell to the plasma membrane and out into the environment around the cell?

Mast cells contain a number of large, granular structures that are regarded as “secretory lysosomes,” yet they share several features in common with large dense-core vesicles, particularly with respect to the mechanisms of exocytosis. Upon activation, mast cells "degranulate" and exotcytose the contents of granules.

SNARE-dependent mechanism mediates exocytosis of neurotransmitters, hormones, and cytokines. Exocytosis of MCG is also SNARE-dependent. SNARE proteins are a family of evolutionarily conserved proteins that facilitate docking of apposing membranes and facilitate the fusion of membranes to accomplish exocytosis. The characteristic feature is a SNARE motif, a stretch of 60-70 amino acids, arranged in heptad repeat. This feature allows SNARE motifs of the individual SNARE proteins (from opposing membranes)  to zipper together, forming a core complex of a four helix bundle. The major SNARE proteins involved in mast cell degranulation include VAMP-8 (integrated in mast cell membrane), SNAP-23 and syntaxin-4 (both plasma membrane bound). There are other layers of regulation of course. The SNARE accessory proteins synaptotagmin 2 (a calcium sensor), Munc13-1/2, Munc18-2 and complexin-2, exert negative or positive modulatory effects on mast cell granule exocytosis (Woska & Gillespie 2012).

EDIT: I don't know about PKC's involvement, but I can speculate that it's part of the signalling pathway after activation of the Fc receptor and upstream of events that initiate mobilization of intracellular calcium, which would then immediately trigger exocytosis. As for movement, if they're like dense-core vesicles, move along actin filaments using a myosin motor (Va or Vb, for example), and in association with Rab-3. This is speculation though, and I'd suggest looking into the literature for more detailed analyses as you are asking for a broad literature review.


How do download a list of the gene length of all genes? I would like to get the gene length information of all the human genes. Is there a quick way to get this information? Thank you!

Some basic information like length can be obtained in the GTF file (you can get the latest ENCODE GTF from the UCSC genome browser).
Other information are also available and obtainable from the UCSC genome browser → table browser. Select the group and tracks that you want from the corresponding dropdown boxes. You can export the data as a text file or forward it to the galaxy interface for analysis.

If you are familiar with some programming then you can pull out the lengths (it is not explicitly given in the output or in the GTF). Also, the gene length may be different from the mRNA length because of the presence of introns in the former. The third field in the GTF file denotes the feature (gene, transcript, exon, etc); you can parse the GTF for picking up only desired features, lets say the mRNAs.
The fourth and fifth fields denote start and end positions respectively; all you have to do is end - start to obtain the length.

A small scriptlet such as this would work in linux/cygwin terminal (I wont go in detail because this is not the scope of this forum):

awk -F "\t" '$3=="transcript"{print $9, $5-$4}' file.gtf > output.txt

The $9 refers to the ninth field which holds information about that feature including the gene name, gene id etc.

The first link that I mentioned also shows some basic methods of extracting information from GTF.


DNA replication in E.coli What is the difference between replication and to divide? My A level bio book says that it takes 20 min for E.coli to divide and in next page it's written that E.coli completes replication within 38min.

Moreover, there is a diagram (shown below) which contradicts as what I thought.

Please explain the difference between replication and division.

Replication refers to DNA replication and division refers to the cell division. Yes it is true that, in E.coli replication can be slower than the division time. This is a well known problem in molecular genetics.

The bacterium copes up with this by having a partially replicated genome during the beginning of the "cell cycle". So there are actually two origins of replication when a new cycle starts. When the replication proceeds you have multiple forks (from the replicated origins). Because of these multiple forks (forks within forks), the replication time speeds up. See the figure below:

 From Fossum et al. 2007

For more details see:

Fossum, Solveig, Elliott Crooke, and Kirsten Skarstad. "Organization of sister origins and replisomes during multifork DNA replication in Escherichia coli." The EMBO journal 26.21 (2007): 4514-4522.

The picture that you have shown is something totally different. As mentioned by Chris, the picture illustrates the Messelson-Stahl experiment to demonstrate the semiconservative nature of DNA replication. Do not confuse that with the above problem. As for the 40min shown from generation-1 to generation-2, in this picture, I feel that it is a misprint.


What happens to dextrorotatory amino acids in humans? As indicated by this question, most of the amino acids in the human body have the L-chirality. As enzymes also have handedness, what happens to the D-amino acids that end up within the human body? Are they simply excreted? Are there enzymes (perhaps not in humans) that convert a D-amino acid to a L- one?

For the most part they are not used.  there are amino acid racemases, which interconvert L- and D- forms of some specific amino acids, which may be used in some particular biosynthetic or metabolic pathways.

In particular I'm thinking of firefly luciferase which uses D-Cysteine as a re-dox reagent to regenerate the luciferin substrate that the light - generating enzyme consumes.  see slide 4 here.

Nonribosomal peptide synthases often use D amino acids too.

I don't believe that d- amino acids are really incorporated into proteins though.


Cell nanoparticle dynamics within blood I am trying to mathematically model the dynamics of a particular cell in circulation and its binding to another nanoparticle that is intravenously injected. The concentration of this cell is very low (about 5 cells per mL of blood). I want to see how many nanoparticles are needed to bind to as many of these rare cells as possible.

So first, I am trying to model the cell dynamics in the blood flow. I am not sure how to start. I wanted to model the cell movement through the entire cardiovascular system, but I would have to simplify it. I am thinking of modeling the blood flow through some of the major organ systems, and estimating the absorption through the capillaries. I am thinking something like the physiologically-based pharmacokinetic model (PBPK). However, there would be some parameters that I wouldn't know about that I would need for the model (at least that is what I think, I am new to pharmacokinetics) Also for the actual fluid dynamics, I'm not sure how to model this, because the blood isn't just a fluid, and has many other cells, so I don't know if there are some other effects.

So, my question is, in what direction should I go to model the dynamics of this cell in circulation? I want to model the circulation in the entire cardiovascular system, because I need to also model the other nanoparticle dynamics, and how likely it is to find and bind to some of the receptors on the cell. Is there an example of a similar model that has been done?

To go the PBPK route:

I would recommend using the organism parameters and structure from the whole body platform model by Shah and Betts.

Shah, D.K. & Betts, A.M. J Pharmacokinet Pharmacodyn (2012) 39: 67. doi:10.1007/s10928-011-9232-2

They have assigned a plasma space volume, plasma flow, blood cell space volume and blood cell flow for each organ and the total body.  The base model structure for circulation is complete if you use the equations for the blood cell space in this paper as the foundation (Eq 2 and Eq 5).

Once the model structure is complete, step 2 is to model all processes that can affect the cell in each compartment.  If the cell is adhering to a nanoparticle, a compartment equation could then be:

d[cell]/dt = (flow in - flow out)/volume + Kon x [nano] x [cell] - Koff x [cell-nano complex]

To model the interaction of the cell with the nanoparticle you will need to model both within the same structure.  A review of PBPK modelling for nanoparticles can be found here:

Physiologically Based Pharmacokinetic Modeling of Nanoparticles
Mingguang Li, Khuloud T. Al-Jamal, Kostas Kostarelos, and Joshua Reineke
ACS Nano 2010 4 (11), 6303-6317 doi: 10.1021/nn1018818

A pharmacokinetic (top-down, classical) model for nanoparticles in the circulatory system may also give insight to how to model the processes that affect nanoparticles in vivo.  This model accounts for fluid dynamics, pore size and specific nanoparticle properties.

Kirtane, A. R., Siegel, R. A. and Panyam, J. (2015), A Pharmacokinetic Model for Quantifying the Effect of Vascular Permeability on the Choice of Drug Carrier: A Framework for Personalized Nanomedicine. J. Pharm. Sci., 104: 1174–1186. doi:10.1002/jps.24302


Are there animals which produce their own colour pigments`? After discovering flamingos natural colour isn't red, pinkish as one naively may have assumed though, I looked into the matter more deeply. I also found out that many other animals do not produce the respective colour pigments matching then their outer appearance.

Some seem to use certain optical effects like Rayleigh Scattering or applying several different layers of filters to absorb wave lengths of light from the spectrum just emitting the intended colour.

After browsing through some more cases several questions arose, which of course cannot be answer all in detail here. However most interesting to me were:

Why does it seem so difficult for animals in contrast to plants to produce their own colour pigments?
Some colours seem to be more difficult to achieve than others. For example I found that melanin and several variation of it as colour pigments are produced quite commonly by animals, however blue rather difficult. As the following post indicates, blue colour pigments seem to be in general difficult to produce: Why are so few foods blue?

Although no expert in this field, I think this question is interesting and I would like to put forward some tentative answers.

In a general evolutionary sense one might regard coloration as a secondary feature of living things — especially animals. Their primary concern is to obtain energy, synthesize structural components, reproduce etc. So the metabolism that evolves under this pressure is such as to allow them to do these things. Colour is not a primary concern. Pigments are complex molecules, and enzymes are only likely to evolve to produce them if there are already reasonably complex precursors available. I know little about plant biochemistry, and would welcome improvement of this answer, but it would seem to me that (1) plants have more complex or different metabolic pathways than animals, such as those for synthesizing chlorophyl, and (2) the pathways for producing pigment precursors are more widespread, perhaps because coloration affords a greater advantage to plants — for pollination etc.

There does appear to be pigment synthesis in animals — an article on pigmentation in bird feathers can be found on the website of The Cornell Lab, for example. That states that the pigments in bird feathers are based on three types of compounds: carotenoids (red or yellow), melanins (black to reddish brown and pale yellow) and porphyrins (pinks, browns, reds and greens).

Two of these are related to compounds the birds synthesize themselves from amino acids — melanins for skin pigmentation, and porphyrins for haem. However, it appears that carotenoids are not synthesized by the birds that employ them for coloured feathers, but are acquired from plants in their diet.

Finally, one might argue that producing colours by optical effects has certain advantages over the use of pigments, namely that they are ‘tunable’ — can be modulated or turned on and off.


Source of DNA sequences I'm working on a project where I am taking DNA sequences and translating the codons into musical notes. I have some good ideas of how to do this, I'm just not sure what sequences to work with. My case study and a lot of my initial research showed that anything larger than a protein is too much to work with for now.

So my question. Where can I find protein DNA sequences in some standard format. I've looked at NCBI but I have no idea what I'm looking at or if I'm downloading the right stuff. Is there a link that I can go to that will have a listing of a bunch of difference protein sequences that I can download?

GenBank and RefSeq have a huge collection of DNA sequences that can be downloaded in Fasta format. GenBank makes it very easy to search for sequences (for example, using the organism name) but will often have redundant data and varied types (everything from whole chromosome sequences to mRNAs to gene sequences to ESTs). RefSeq has much cleaner, non-redundant data but might take a little more effort for you to find the sequences you want. Depending on whether this has any effect on your project, you might want to consider that. On the RefSeq page, under the FTP menu you can click Genomes to see which genomes have RefSeq data available. The Fasta sequences for a particular genome will be stored in a dedicated directory, possibly subdivided into further directories by chromosome. What you want are the Fasta files (ending in .fa, .fasta, .ffn, or something like that), keeping in mind they may be compressed (.fa.gz, fasta.gz, etc).

Alternatively, if you already have a specific organism in mind, then you could do a Google search to see if the genome for that organism has been sequenced. If so, there is almost always a dedicated website where you can download DNA sequences for that genome.


Why doesn't the cell membrane just...break apart? Forgive me if this is a silly question. I can't understand the basics. Why doesn't the cell membrane just break apart? What's keeping the layers in the phospholipid bilayer together? I know that the membrane is embedded with proteins and lipids, but I still can't wrap my head around the "why". Are the hydrophobic interactions in the middle "stronger" than the hydrophilic interactions on the outside? What's keeping the individual phosphate heads together instead of, say, one of them just drifting away due to a nearby water molecule?

The membrane bilayer is held together by hydrophobic forces. This is an entropy driven process. When a greasy or hydrophobic molecule is suspended in water, the water molecules form an organized "cage" around the hydrophobic molecule. When two hydrophobic molecules come into contact, they force the water between them out. This increases the entropy because the freed waters don't need to be organized into the cage. Lipid bilayers have many many many hydrophobic lipids that squeeze out a lot of water and greatly increase entropy. The polar phosphates allow the water to interact with the surface of the membrane, without a polar head group the lipids would form a spherical blob instead of a membrane.

Read this section on wikipedia for more.


Moth with silver marking on wings This is a moth that we found on a curtain inside the house a couple of days ago. Unfortunately, these pictures did not come out as well as I thought before I realized it outside. But I was struck my the silver-white eyeglass-shaped spots on the wings. It also had an interestingly shaped head, but that didn't come out well. The closest I have come to identifying it is that it looks similar to a Dot Moth, but those don't seem to be native to Southern California (Los Angeles).

It was about an inch long, maybe less. It vibrated its wings after I disturbed it.

Based on the overall apparence and the distinctive metallic patches on the wings it looks like a moth from the subfamily Plusiinae (Looper moths). I'm not familiar with North American moths, but after a quick check at species found there Megalographa biloba (Bilobed looper moth) seems likely, and this species is also found in California.

(picture from wikipedia)

Also see the pictures at Bugguide.net.


Best fundamental books? I’m looking for internationally applauded  textbooks on fundamental biology. Books that are a must for a pre-medicine student/high school advanced. Currently, I study Biology by Neil Campbell, Jane Reece(and team) and I really like it. What I’m looking for is 21st century pedagogy and a modern writing style(as opposed to a stiff, unfriendly writing style that reads like a fact presentation pamphlet); books so good you don’t need an amazing teacher(which I definitely do not have.) Thanks.
P.S.- If you have come across amazing books in branches of biology like say biochemistry or neuroscience or immunology, even those suggestions are welcome.
P.P.S- My question is distinct from the “Books for beginners” question asked by user31782 because: 1.cost is no bar 2.I am not a beginner in biology, I’m studying pre medicine; and 3.All the resources suggested in the answers, I already know about them/have used them.

For fundamental mammalian cell biology, and molecular biology, and fundamental biochemistry: "The Molecular Biology of the Cell" by Bruce Alberts and colleagues.

It is mostly written for first semester students at university and thus summarizes the basics in a very clear way. Moreover they state whenever findings have some ambiguity, and they use many nicely drawn pictures to convey abstract concepts.  Despite its approachability it covers most fundamental topics of many domains (also diseases).

While the ~2,000 pages of the complete edition might seem a bit intimidating they rarely provide unnecessary detail, and the individual chapters are written in a very concise way (even allowing you to skip some of them).


Applying kiwis on gelatin Kiwis have the enzyme actinidain. This enzyme will break the peptide bonds from the gelatin. Making gelatin with raw kiwis will not work, because the peptide bonds in the gelatin will be broken down.

But what if you would make plain gelatin, and apply raw kiwis to it? Do the enzymes break down the gelatin when the gelatin already has set?

According to the (non peer reviewed) scientific experiment found here, simply placing a piece of kiwi onto gelatin that has set will cause the gelatin to be hydrolysed by actinidain.

  This experiment aims to show the effects of Proteolytic enzymes on proteins and, subsequently, the effects of extreme temperatures on the proteins themselves. Petri dishes filled with gelatin, a derivative of collagen, were acted upon by kiwifruit samples overnight. Some samples were fresh and used as controls; others had been frozen or boiled for two, four, six, eight or ten minutes. The mass of digested gelatin was taken the next day. The results ultimately reflect the effectiveness of the actinidin, the kiwi’s Proteolytic enzyme, under normal conditions and after exposure to extreme temperatures.


Nature Scientific Reports vs. BMC Genomics I do not know if this question to suitable here or not. I posted it as I think biologists can help me in this question. If not suitable here, then I am sorry for that.

I have written paper which I spent about 3 years working on it and it has nice findings and original sequenced data (deposited in NCBI). I submitted the paper to "Genome Biology" and I got editorial rejection but they offered to transfer the paper to "BMC Genomics". However, my supervisor refused this and suggested that we submit to "Nature Scientific Report". I tried to convince him to go to BMC Genomics because it is more focused journal and it is better for my CV, however, he said the second one is better because it has better impact factor and it is Nature! (Impact factor: 5 for Scientific Reports vs 4.04 for BMC Genomics).

What do you think as I am really confused which one to select?

This is too long for a comment, so I post it here. And these are my personal views, someone else might handle this different. I would submit the paper to BMC Genomics for some reasons:

The editor offered to transfer the paper, so you get past the
editorial review. This is not guaranteed for Nature Scientific Report
(NSR). You still have to get through the peer review, but this is not
different between both journals.
Honestly: Forget about the difference in the Impact Factor. Both are
medium range impact factor journals closely located together. My most
cited paper is published in such a medium impact journal, today you
find papers by a Medline search, so this doesn't matter anymore
(besides prestige). Additionally a lot of citations will raise the
journals impact factor in the future. I would understand this
argument when you would have to choose between Nature and BMC
Genomics, there is quite a difference.
If your work fits better into BMC Genomics the chance for acceptance
is higher, so I would go there. This is of course always a point of
consideration. The same is true for your CV.

If you have the chance to do the decision for yourself without angering your supervisor too much, I would go for it. Even better would be to convince him.


Do the four cells produced by meiosis each divide into four cells again? In the beginning of meiosis, there is one cell. During meiosis, 1 cell divides into 4 cells. Does each of these 4 cells divide each into 4 more cells?

No, meiosis is not a cycle like mitosis. In mitosis, haploid or diploid cells divide to create two genetically identical cells, and this process can go on and on. On the other hand, meiosis results in 4 genetically unique daughter cells which are also haploid. If a haploid cell was to try to undergo meiosis, there would not be enough genetic material and you would end up with half-chromatids.


What is a partial regulator? Source: MY textbook-NCERT 12th Biology-Ch: Organisms and Population
(Pg 7 of pdf/Pg 223 of the book)

Is this graph for Partial regulators correct? Isn't it that animals tend to be regulators first and then when they can't maintain homeostasis anymore, they tend to conform aka adapt themselves to the surrounding for better survival?

So shouldn't the graph for Partial Regulators first be a straight-line parallel to the axis (signifying constant internal environment aka Homeostasis) upto certain External surroundings level and then be the inclined straight line when it behaves as conformer ?

I would like to know where I am wrong in my logic or Is it that The graph is wrong in my book ?

I think, the graph you indicated, might saying the following matter:
Let's take an example. " Some snails and fish  go into aestivation  to avoid summer-related problems-heat and dessication."  Now, when summer comes after the season Spring, the temperature gradually rises. The fishes can generally  withstand upto a threshold limit of temperature, and conforms upto this threshold limit. When their   comfortable weather breaks due to rising temperature, then they enter Aestivation and the graph now starts paralleling the X-axis.
Look, the graph doesn't parallel to the " Conformers' line" from the origin, but deviates with a little angle from that line : that implies the organism was trying to regulate against the external environment at first.
Undoubtedly, it's my own opinion, may carry some shortcomings generally.


Why cancer disease is named after sun signs ? I googled it, It didn't helped me a lot.

So Why cancer disease is named after sun signs ?

It isn't. The name of the constellation/zodiac sign and of the malignant cell diseases comes from the Latin word "cancer", which means "crab".

This name for the disease dates back to the Greeks and Hippocrates, who used the word "karkinos" (the Greek equivalent) because the veins around the tumors they observed made the disease look like a crab 3.


What type of bee/wasp is this? I found some bees or wasps, in my garden.

Auckland, New Zealand
13mm long head to abdomen, fluffy on thorax and head. Abdomen is orange brown with black stripes.

The nest or hive is underground (otherwise I'd suspect honey bee, though they seem a little smaller even than honey bee workers).

I managed to catch one eventually, but then I realised the container had oxide powder, so the bee in the attached picture is a lot blacker than it was in life. It is also dead ( just in case that's not obvious)

They don't seem to be aggressive - there is a new fence being built right past their nest, they don't seem to be bothered by it.

I am a beekeeper but only beginning, so I do have honeybee workers to compare it to, but not a whole lot of experience.

NOTE: it is autumn (fall) here - high temperature was 23° c (73° f)

It is a vespid wasp (family vespidae). Bees are generally hairy, and this one has the typical wing folding of a vespid. Genus Vespula. There is a New Zealand website that shows the differences among common NZ wasps here:
https://www.landcareresearch.co.nz/science/plants-animals-fungi/animals/invertebrates/invasive-invertebrates/wasps/identification/key-differences


External tissues, connected to the body? Some cancer tumors suppress themselves from spreading. When such tumors are removed by surgery, the metastasis process is accelerated.

Isn't it possible to put such tumors into external device like hemodialysis device and slow metastasis process this way?

Are there any experiments or clinical usages of own body tissues in such a devices? Not for cancer, but probably for some other reasons, in humans and animals?

Some sort of grafting for animals.

Such a tissue can interact with main body by blood and cause some effects.

I've actually wondered this myself from time to time, without ever bothering to look it up.  Well, it's actually happening.  That WSJ article says the following, which just blows my mind:

Researchers at the Rogosin Institute are taking tumor cells from mice, encapsulating them in beads made from a seaweed-derived sugar called agarose, and implanting them in the abdomen of cancer patients. There, cells in the beads secrete proteins researchers believe could signal a patient's cancer to stop growing, shrink or even die.
So far, at least 30 patients have been treated with the cancer beads in an initial human study, and a phase two or intermediate-stage trial has been launched—with the approval of the U.S. Food and Drug Administration—to test the technique in patients with advanced colon, pancreatic and prostate cancers.

You can find the info on the Phase II trial here; they are currently at the "recruiting participants" point.

[The treatment] consists of small beads that contain mouse cancer cells from a mouse kidney cancer cell line. The cells in the beads produce substances that have been shown to slow or stop the growth of tumors in experimental animals, veterinary patients, and 23 humans with different types of cancers in a Phase 1 safety trial.


How does the body switch between aerobic and anaerobic respiration? Lets take the case of a person doing heavy exercise. Aerobic respiration is taking place, but oxygen is about to be finished up. Glycolysis occurs, Krebs cycle finishes. Now NADH and FADH2  enter electron transport system (ETS) to form ATP, but at the last step, cytochrome c oxidase cannot get oxygen as it just finished up. Now, what happens to the ongoing ETS? Does it go in reverse order and then arnon cycle to get back Acetyl co-A and respire anaerobically, or does this process get paused and respiration switches over to anaerobic mode till oxygen supply is replenished?

The simple answer to your question is that in the absence of oxygen the electron transport chain stops. (It can't go backwards, that would generate oxygen.) However your assumption that it stops at the last step is incorrect, all the cytochromes are converted to their reduced form, and there is feedback that diverts the NADH elsewhere.

The situation is complicated because it depends what tissue you are talking about and what sort of exercise and what is the fuel for respiration. However let us consider the skeletal muscle at the start of a non-sprint run. Let us assume that it will be using glycogen as a source of fuel, which is converted to pyruvate and NADH. The pyruvate will enter the tricarboxylic acid (TCA) cycle in the mitochondria and be oxidized there and also produce metabolites. The NADH from glycolysis (produced by reducing NAD+) will enter the mitochondria and be oxidized; however it does not enter directly but via a shuttle, one of which — the malate-aspartate shuttle, show below — will be considered in a more detail lower down.

Now let us suppose there is a sudden need to sprint so that the muscle cannot get sufficient oxygen to deal with the NADH produced in glycolysis. What happens? The key event is that pyruvate is oxidized to lactate. Why? Not because lactate is useful, but because this is an anaerobic means of oxidizing the NADH back to NAD+ to allow glycolysis to continue and ATP to be produced at the substrate level.

Why doesn't the NADH keep going into the mitochondria (where it would be wasted as the electron transport chain has stopped)? Because the shuttle stops — in the case of the malate-aspartate shuttle mitochondrial malate dehydrogenase stops converting malate to oxaloacetate, malate builds up and therefore the malate transporter stops bringing malate into the mitochondrion.

This can be understood at the most general level by the fact that if NADH in the mitochondrion cannot be oxidized it will accumulate, hence slowing and eventually arresting the malate dehydrogenase reaction by simple mass action.

In fact Nature generally uses more sophisticated regulation that allows switch on and switch off to be performed more rapidly and completely, most notably by allosteric regulators. In the case of malate dehydrogenase the situation is not really clear, but there are reports that suggests citrate is an allosteric activator of the enzyme in some tissues (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1131027/). The concentration of citrate falls as the TCA cycle stops because of the lack of NAD+ (this is because TCA cycle intermediates get tapped off for other purposes) so the activating effect of this intermediate would be removed.

(There is another shuttle for reducing power that my be more important in skeletal muscle. This is the glycerol 3-phosphate shuttle. However as this requires the oxidized form of FAD directly in the mitochondrial membrane it will clearly shut down in anoxia.)

The net result is that the NADH stays in the cytosol to be oxidized by pyruvate in the lactate dehydrogenase reaction.

This can only happen if the pyruvate stays in the cytoplasm and does not move to the mitochondrion. Obviously the lack of NADH to reduce it to acetyl-CoA in the pyruvate dehydrogenase reaction would cause its concentration to build up in the mitochondrion and reduce transport across the membrane by simple mass action. However it is likely that the specific mitochondrial pyruvate transporter is regulated by metabolites which change their concentration under these conditions. The evidence here is indirect as the transporter was only identified and cloned in 2012.


Why do crows sit on treetops even when it is cold? It is cold outside: -1 degrees Celsius, wind 14 km/h and snow from time to time. I was wondering why crows (maybe birds in general in Northern Europe) are calmly sitting in relatively windy places even though there are plenty of potentially warmer places to go to. (see picture at the bottom).

My first guess was that it isn't cold enough for them However, I couldn't find support for this online, so it's not possible to know for certain.

NB1: This is my first post - let me know if something is inappropriate.
NB2: I am not a biologist, so please be patient.

I'd appreciate links/references where I could get information that gets closer to finding an answer to the given question.

Birds (crows inclusive) have better heat conservation adaptations as compared to humans. Some of these are (but not limited to):

-Hollow tubes in feathers which provide insulation reducing heat loss.

-Reduction of appendage length especially in species that dwell in cold regions.

So conditions we perceive as cold are relatively warm for birds.

  My first guess was that it isn't cold enough.

From this question on biology.se I can say it could be warm for them as it addresses birds surviving at -40C. Plus some of the answers and comments on the same question cover a couple of adaptations that birds exhibit to strive in such conditions.

edit: links that provide additional information on the same

-http://toughlittlebirds.com/2012/12/26/how-do-birds-keep-warm/
-https://beyondpenguins.ehe.osu.edu/issue/arctic-and-anarctic-birds/how-do-birds-stay-warm
-http://birding.about.com/od/birdingbasics/a/howbirdskeepwarm.htm
-http://gardenwalkgardentalk.com/2013/02/19/how-do-birds-keep-warm-in-winter/


Is there evidence that children should play in dirt to get healthy? I've heard it said many times, that we should let children play in the dirt as it builds up their immunity and prevents things like allergies in later life.

I have another suggestion which, to me, is equally plausible. In older times when families had lots of children, and they used to play in the dirt, those weaker children used to get ill and die. Leaving the `stronger' children who were less suceptible to allergies and diseases to grow to adulthood.

So in our cleaner lifestyles where we prevent our children from playing in the dirt, actually we are just letting children who would normally have died off early grow to adults. (Which is a good thing from a moral standpoint - although overall it means the human population as a whole grows weaker in the short term).

Therefor telling people to let their children play in the dirt is bad advice if this is true.

Which of these two options do you think is the truth?

(Mathematically, let us assume that by random chance 50% of babies have bad immunity, but that parents have an average of 4 children. This means if half the childen die in childhood, the adult population would be full of people with good immunity. This is my terrible conclusion which has no moral solution.)

This answer focuses primarily on allergies, for which there is more reliable research, but touches on general immunity towards the end.

It is certainly true that the prevalence of allergies is increasing worldwide, and seems to be related to a rise in the so-called 'modern lifestyle' which avoids exposure to potentially harmful environmental factors.

  The prevalence of allergic diseases and asthma are increasing worldwide, particularly in low and middle income countries. Moreover, the complexity and severity of allergic diseases, including asthma, continue to increase especially in children and young adults, who are bearing the greatest burden of these trends. - World Allergy Organisation Journal

The idea that playing in the dirt builds an individual's immune system and reduces the chances of allergies etc. is known as the "hygiene hypothesis" (or, more accurately, the hygiene hypothesis states that

  due to reduced exposure to microbial components, the proposed allergy-preventing potential of these factors is no more present in sufficient qualities and/or quantities, which leads to an imbalance of the immune system with a predisposition to the development of allergic disorders." - Epidemiological and immunological evidence for the hygiene hypothesis.

)

Aside from potential mechanisms, there is certainly evidence for the hygeine hypothesis

  The researchers studied the immune system of mice lacking bacteria or any other microbes ("germ-free mice") and compared them to mice living in a normal environment with microbes.
  They found that germ-free mice had exaggerated inflammation of the lungs and colon resembling asthma and colitis, respectively. This was caused by the hyperactivity of a unique class of T cells (immune cells) that had been previously linked to these disorders in both mice and humans.
  most importantly, the researchers discovered that exposing the germ-free mice to microbes during their first weeks of life, but not when exposed later in adult life, led to a normalized immune system and prevention of diseases.
  Moreover, the protection provided by early-life exposure to microbes was long-lasting, as predicted by the hygiene hypothesis. - Microbial Exposure During Early Life Has Persistent Effects on Natural Killer T Cell Function

As far as I know there is no consensus on this issue, however a number of scientific studies have proposed potential mechanisms to explain the rise in allergies and other such conditions; one of the most widely accepted ideas is that an avoidance of germs and microbes early on in life leads to

  changes in the fine balancing of T helper cell 1 (Th1), Th2 and regulatory T cell (Treg) responses which are triggered by altered or missing innate immune cell activation. In fact, proper activation of cells of the innate immune system via their so-called pattern recognition receptors has been demonstrated to play a crucial role in early shaping of the immune system and suppression of the development of Th2-driven allergic immune responses. - Epidemiological and immunological evidence for the hygiene hypothesis.

this would seem to explain the observed phenomena.

It is definitely true though that there has been and will continue to be an element of natural selection involved here, as you have pointed out, because it is a force that is found pretty reliably in these sorts of situations. It is certainly logical that exposure to microbes during infancy will help weed out those with a weaker immune system (assuming they died because of infection/disease etc.), which over time would create a population and species that was more resilient. However, I can't find any studies to back up this idea. It is also a somewhat separate issue to the idea of the hygeine hypothesis, which describes changes to a specific individual within their lifetime rather than necessarily across a population due to natural selection and evolution, which is the explanation you have provided (unless I misunderstand your point?).

I only have a general understanding of immunity, however it is generally accepted that exposure to a pathogen (if this episode is survived) will result in an immune system which is better able to counter that pathogen in the future - this is the whole concept of vaccinations. therefore it makes sense that, again, low levels of contact with 'germs' will build a child's immunity.

Overall I think that it is a complex issue without a generally accepted answer as yet, however it seems to me based on this research that "playing in dirt" (in other words, being exposed to low levels of pathogens, microbes and toxins) does in fact build immunity and reduce the likelihood of developing allergies in later life, even if we don't know the exact mechanism for this yet.

aside from any potential immunity benefits, most children find playing in dirt fun (I know i did), so for the most part i'd say let them do it anyway!

My sources:

https://www.sciencedaily.com/releases/2012/03/120322142157.htm
https://www.ncbi.nlm.nih.gov/pubmed/17544829
https://waojournal.biomedcentral.com/articles/10.1186/1939-4551-7-12


Program (on Mac) to show 3D protein structures? I have an assignment for 6th grade biology. I have to look at a 3D structure of a protein and manipulate it so it only shows the AA I’m interested in currently.

what I already did
I already looked up the programs most used for this and they point me to JMol and Yasara but the download files are .bin files and the like and I don’t I don’t understand which file is the one I should download and how to install it.

Can someone help me please ?

Jmol: how to install

Here are instructions for getting Jmol to run on a Mac (or with a slight variation in the runtime file you need to download and the security warnings, on a PC).

Download Jmol from
https://sourceforge.net/projects/jmol/files/latest/download?source=files
The name of the file will be something like Jmol-14.29.16-binary.zip. Double-click to unzip.
The unzipped folder has a confusing variety of files. This is because most are used for setting up web pages with Jmol embedded. However there is a double-clickable desktop application without any icon and the unpromising name of: Jmol.jar. When you double-click to launch it you will most likely get a message as shown below (1):

To get round this you must either control-click or right-click and select `Open With > Jar Launcher as shown above (2).

Click ‘Open’. (Next time it will just launch without right-clicking.)

Now, in my case the program launches because I have the Java runtime installed on my machines, but you will probably have to download and install this.
Go to the Oracle Java website at http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html
Download and install the appropriate Java SE Runtime Environment, e.g jre-8u172-macosx-x64.dmg
Try launching jmol.jar again. It should work this time.

Jmol: how to use

Because of their emphasis on Jmol in relation to the web, the developers of Jmol do not provide an easy entry to the desktop program. However you can find a clearly illustrated series of web tutorials at the MSOI Centre for Biomoleclar Modelling. I’d highly recommend this as a starting guide.

Although I am not going to describe how you can visualize particular amino acids as that is part of the poster’s project and can be found in the instructions. there are a couple of pointers I would make about things that are not entirely obvious.

After you have loaded a protein from the file menu, you will probably want to change its representation, not least because it may be surrounded by red balls (oxygens from water). To do this you need to right click (or click on the Jmol text on the bottom right) and go through two levels of submenus to select an appropriate representation, as shown.

In order to make the selections you require you will need to issue commands in the ‘Console’. This can be selected from the File menu:


How dissimilar are the fingerprints of identical twins? It is a very well-known fact, stated multiple times even in this Stack Exchange, that identical twins have different fingerprints. However, to what specific extents, and in what specific ways, do the sets of fingerprints of identical twins typically differ? Are the differences usually very minor (e.g., just a few stray loops and whorls here and there)? Are they perceptibly different but still fairly similar, with the similarities most likely stemming from heredity and/or cultural ties? Or does the determination of fingerprint patterns behave similarly to a uniformly weighted random number generator, with the fingerprint sets of twins being just as different as those of two people born on opposite sides of the world?

Obviously, due to the random/probabilistic nature of this feature, there may be no single answer to this question — there may be cases where one pair of twins has fingerprints that are more similar than those of another pair. But does anyone know what typical similarities and differences are present between the fingerprint sets of identical twins, and, if possible, the biological causes of such similarities and differences?

Identical twin fingerprints are different, but generally more similar than to random people.  For example:

  Fingerprint recognition with identical twins is a challenging task due to the closest genetics-based relationship existing in the identical twins ... Srihari et al. [6] analyzed the similarity between twins' fingerprints in a study using fingerprint images from 298 pairs of twins. The authors analyzed this similarity using two-level features. With the features of level 1, they found that twins' fingers are much more likely (55%) to have the same pattern type than non-twins' fingers (32%). With the features of level 2, they concluded that the similarity between the fingerprints from twin fingers is higher than from two arbitrary fingers.

Fingerprint Recognition with Identical Twin Fingerprints

  Dermatoglyphic asymmetry and diversity traits from a large number of twins (MZ and DZ) were analyzed based on principal factors to evaluate genetic effects and common familial environmental influences on twin data by the use of maximum likelihood-based Variance decomposition analysis. ... The present results are similar with the earlier results of finger ridge count diversity in twin data, which suggested that finger ridge count diversity is under genetic control.

--Inheritance of dermatoglyphic asymmetry and diversity traits in twins based on factor: variance decomposition analysis