What is the difference between nucleotide polymorphism (θ) and nucleotide diversity (π)? In my population genetics book (see reference at bottom) they define them as:

Nucleotide polymorphism (θ): proportion of nucleotide sites that are expected to be polymorphic in any sample of size 5 from this region. Of the genome. $\hat{θ}$ equals the proportion of nucleotide polymorphism observes in the sample (S) divided by $a_1 = \sum_{i=1}^{n-1} \frac{1}{I}$. If n= 5, $a_1 = \frac{1}{1}+ \frac{1}{2}+ \frac{1}{3}+ \frac{1}{4}+ \frac{1}{5}=2.083$
Nucleotide diversity is the average proportion of nucleotide differences between all possible pairs of sequences in the sample. In R, I came up with that code which is in accordance with what is in the book.

   data # Only polymorphisms
   total.snp # This is the total number of sites that were looked (e.g. 16 might be polymorphic over the 500 sites that we've looked at. So 484 sites are monomorphic)

   n = nrow(data) # Number of samples
   pwcomp = n*(n-1)/2 # Number of pairwise comparisons
   for(i in 1:n.col){ # Compute the number of differences in the samples that are polymorphic
     t.v = as.vector(table(data[,i]))
     z = outer(t.v,t.v,'*')
     temp= c(temp,sum(z[lower.tri(z)]))
   }

   pi.hat = sum(temp)/(pwcomp*total.snp) # Nb of different pairwise comparison/(nb all pairwise comparison * total nb of loci (polymorphic or not))

In the book, they say

  On the other hand, there is a theoretical relation between θ and π that is expected under simplifying assumption that the alleles are invisible to natural selection.

In summary θ = π with this assumption and large sample sizes.

So what is the difference in the
Why are we calculating both
(what could they tell us)?

Hartl, D. L., & Clark, A. G. (1997). Principles of Population Genetics (3rd ed.). Sinauer Associates Incorporated.

You are also confusing definition of these terms with their expected values (typically computed from coalescent theory). Let's look at an example.

Consider a haploid population of 6 individuals. We will represent these individuals with 5 sites that can take values 0 or 1.

00000
00001
00000
00010
00010
00000

Polymorphism

In this population there are $S=2$ polymorphic sites. In other words, there are two sites for which different individuals take different values in the population. Over these 5 sites, the fraction of polymorphic sites is $\frac{2}{5}$. You use $\theta$ for this quantity but to me, $\theta$ is typically used as a short hand for $2 N \mu$ (or $4 N \mu$ for diploid populations).

Under an infinite allele model, in a single panmictic haploid population (without selection and other assumptions), $E[S] = 2 N \mu a$, where $a = \sum_{i=1}^{k-1} \frac{1}{i}$, where $k$ is the sample size.

Genetic diversity

Genetic diversity is also known as expected heterozygosity. While it is most often called $\pi$, I will call it $H$ to avoid confusion. Imagine, you randomly sample two individuals in the population, what is the probability that there have different alleles at a given locus?

At locus 1, $H = 0$
At locus 2, $H = 0$
At locus 3, $H = 0$
At locus 4, $H = 2 \frac{2}{5} \frac{3}{5} = \frac{12}{25}$
At locus 5, $H = 2 \frac{1}{5} \frac{4}{5} = \frac{8}{25}$

You can average over all loci if you want.

The expected heterozygosity in panmictic population (without selection and other assumptions), $E[H] = \frac{4 N \mu}{1 + 4 N \mu}$. You should notice a relationship between $H$ and $F_{ST}$ here!

Nucleotide diversity

The nucleotide diversity is the equivalent of $D$ from Nei and Li (1979) and is highly related to $D_{XY}$ (Nei, 1987). Once you've managed to demonstrate that the expected coalesence time is $N$ (I won't do the demonstration here), then under an infinite site model, the number of mismatch between two individuals is logically $E[D] = 2 N \mu$ (it is the number of mutations that has happened in both lineages since the the coalescence event). For diploid population, multiply everything by 2.

Relatedness between $D$ and $S$

Under a neutral model $\frac{S}{a} = D$. Actually the standardize difference between $\frac{S}{a}$ and $D$ is what is used in Tajima's $D$ tests.

Source of information

Hartl and Clarck is good IMO but I would also like to recommend reading Population Genetics: A Concise Guide by Gillespie who explain all of that wonderfully.


What is the smallest number of amino acids required for life? Is there any hypothesis on the minimum number of amino acids required for life?

You can divide the 22 (including selenocysteine and pyrrolysine)  proteinogenic amino acids into broad groups of similar amino acids. There are the hydrophobic amino acids like trypthophane, valine and leucine, the charged amino acids like glutamate and arginine and the polar amino acids like serine and threonine. There are some amino acids with unique features like cysteine which can form disulfide bonds.

Some amino acids are very similar, for example isoleucine and leucine, it is plausible that one of those would suffice to create most protein folds.

There are several examples of proteins designed with a smaller alphabet of amino acids, one example is the E. coli orotate phosphoribosyltransferase (Akanuma et al., 2002). The simplified enzyme consists of only 13 different amino acids and 88% of it are composed of only nine different amino acids. Even after those drastic changes the enzyme still folds correctly and has enzymatic activity.

There is one study (Fan and Wang, 2003) that tried to answer exactly the question you asked. They came to the conclusion that around 10 amino acids are necessary to create properly folding proteins:

  First, we study the minimum sequence complexity that can reserve the
  necessary structural information for detection of distantly related
  homologues. Second, we compare the ability of designing foldable model
  sequences over a wide range of reduced amino acid alphabets, which ﬁnd
  the minimum number of letters that have the similar design ability as
  20. Finally, we survey the lower bound of alphabet size of globular proteins in a non-redundant protein database. These different
  approaches give a remarkably consistent view, that the minimum number
  of letters required to fold a protein is around ten.

Akanuma, S., Kigawa, T. & Yokoyama, S. Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set. Proceedings of the National Academy of Sciences 99, 13549 -13553 (2002).

Fan, K. & Wang, W. What is the minimum number of letters required to fold a protein? J. Mol. Biol. 328, 921-926 (2003).


Why do ants live so long? I was surprised to learn that worker ants in some species live many years. I would have expected a lifespan of a few weeks or months (which is apparently the case for many species).

What factors might account for the length (and/or variation) in ants' lifespans?   (ie, is there some evolutionary preference? Some fundamental limit on the reproductive capacity of the queen?) Is there any relationship between these lifespans and different structures of ant communities?

There will always be a tradeoff in terms of resource allocation between reproduction and self maintenance. Since worker ants forego reproduction to perform other roles (gathering resources, caring for young etc.) within the colony, it makes sense that this would favour a longer lifespan. This idea works for most animals (i.e. higher reproduction = lower lifespan across species in general) and is well documented (Partridge et al. 1987, Gems & Riddle 1996 (PDF link), Westendorp & Kirkwood 1998 - to name a few). However the relationship is reversed in eusocial animals: the queens of ants, some bees and naked mole rats (which are all eusocial) tend to be longer lived than their sterile workers (Hartmann & Heinze 2003). Aging patterns within ants and other eusocial organisms are a very popular research topic at the moment, but the mechanisms causing differences between social castes are not fully understood.

Eusociality is strongly associated with increased lifespan, indeed many studies on the evolution of aging have focussed on eusocial animals which have appeared to overcome aging effects to an extent (Keller & Genoud, 1999, Buffenstein 2005). The naked mole rat is one of very few species of eusocial mammals and the relationship between its lifespan and body mass is very dissimilar to that of other rodents (ignore the bat points):

Image from Buffenstein & Pinto (2009).

If a queen has a longer reproductive lifespan then over the course of its life it will create a higher number of offspring. This will cause their increased longevity genes to be more prevalent in the gene pool over time - as long as they are able to reach the limit of their reproductive lifespan and are not killed by externalities (accident or attack) in the meantime. Therefore this trait (longer reproductive lifespan) will be selected for as long as the queen is protected.

Within eusocial colonies, there is often a protective environment (Buffenstein & Jarvis 2002): there is usually a physical structure (nest or burrow); symbiotic bacteria and/or fungi creating a more hygienic microflora; and queens are also protected by other castes. This gives queens a lower incidence of death due to accident or attack which (from the reasoning in the previous paragraph) supports the selection of a longer reproductive life. This is likely to lead to longer lived workers since they share the same genes.

However queens do tend to live much longer than their workers (O'Donnell & Jeanne 1995). This is probably due to their reproductive role. All the ants in the colony are investing in reproduction (whether by physically giving birth to young or by providing it with food and protection) therefore the normal relationship (reproduction and lifespan tradeoff) mentioned at the start is not relevant, but since the queen is the only individual reproducing, it will be the only one for whom lengthened lifespan is beneficial evolutionarily.

A mean lifespan of 20 years has been observed in Formica exsecta, and a maximum lifespan of 28.5 years observed in Lasius niger. Pogonomyrmex owyheei has an observed maximum of 30 years, and mean of 17 years. These (and many more) figures were obtained from a review by Keller (1998).

Other references on this subject include (Svensson & Sheldon 1998), (Keller & Genoud 1997) (PDF link), (Calabi & Porter 1989), and (Amdam & Omholt 2002).

References

Amdam, G.V. & Omholt, S.W. (2002) The Regulatory Anatomy of Honeybee Lifespan. Journal of Theoretical Biology, 216, 209–228.
Buffenstein, R. (2005) The naked mole-rat: a new long-living model for human aging research. The Journals of Gerontology Series A: Biological Sciences and Medical Sciences, 60, 1369–1377.
Buffenstein, R. & Jarvis, J.U.M. (2002) The Naked Mole Rat--A New Record for the Oldest Living Rodent. Sci. Aging Knowl. Environ., 2002, pe7.
Buffenstein, R. & Pinto, M. (2009) Endocrine function in naturally long-living small mammals. Molecular and cellular endocrinology, 299, 101–111.
Calabi, P. & Porter, S.D. (1989) Worker longevity in the fire ant Solenopsis invicta: Ergonomic considerations of correlations between temperature, size and metabolic rates. Journal of Insect Physiology, 35, 643–649.
Hartmann, A. & Heinze, J. (2003) Lay eggs, live longer: division of labor and life span in a clonal ant species. Evolution, 57, 2424–2429.
Keller, L. (1998) Queen lifespan and colony characteristics in ants and termites. Insectes Sociaux, 45, 235–246.
Keller, L. & Genoud, M. (1997) Extraordinary lifespans in ants: a test of evolutionary theories of ageing. Nature, 389, 958–960.
Keller, L. & Genoud, M. (1999) Evolutionary Theories of Aging. Gerontology, 45, 336–338.
O’Donnell, S. & Jeanne, R.L. (1995) Implications of senescence patterns for the evolution of age polyethism in eusocial insects. Behavioral Ecology, 6, 269–273.
Svensson, E. & Sheldon, B.C. (1998) The social context of life evolution history. Oikos, 83, 466–477.


Can an attenuated virus cause infection in some rare cases? I just read in some comments, that some children got measles one week after getting the MMR shot. Afaik. MMR contains attenuated live virus, and the incubation period of measles is 10 days (+/- ? days). Can we be certain, that they didn't get infected by the vaccine?

There are two possibilities for getting the measles directly after a vaccination:

The kids where infected shortly before the immunization. Since it takes about two weeks to develop humoral immunity, it is possible that these two events overlap. The measles have an incubation period of 7 - 21 days (see reference 1), with a rash occuring around day 14. So if the kid was around day 7 of his infection, this would fit.
Since the measles vaccination is a live attenuated virus, it is possible to get a rash from it. However, these are relatively rare cases (depending on the source between 2 and 5%) and the infection is mild and not contagious. See also reference 2.

References:

Measles (from the CDC)
Measles: Questions and Answers


ATP utilized in Glycolysis vs. Gluconeogenesis In glycolysis, the conversion of glucose to pyruvate results in a net gain of 2 ATP molecules. In gluconeogenesis however, the conversion of pyruvate back to glucose requires 6 ATP molecules.  Why does there seem to be an apparent loss of energy?

This energy is not lost, it is dissipated as heat.

And this must happen because of thermodynamics -- the direction of the reaction is simply determined by the difference of energy between substrates and products, and it must be positive for the reaction to happen spontaneously.


Have scientists ever produce a new species in laboratory by means of natural selection? I was wondering, if scientists ever produce a more complex species from a less complex species by means of natural selection? I imagine something like, bacteria which can't photosynthesis and oxygen (chemoautotrophs) to bacteria that can photosynthesis and oxygen like cyanobacteria.

If scientists have never done this, is this theoretically possible to be done in lab by means of natural selection?

There are a few issues your question brings up.  First, the idea that species evolve from simple to complex is actually not a prediction or inevitable consequence of evolution by natural selection.  The terms "simple" and "complex" themselves are ill-defined.  For instance, if you defined "complex" to be size of the genome, the most complex organism found to date is probably a flowering plant from Japan.  This idea of arranging organisms from simple to complex hearkens back to a pre-Darwinian idea of the Great Chain of Being.

You may be thinking that since multicellular life, for example, evolved from single-celled organisms, mutlticellular life is more complex than single celled life.  The fallacy is that modern single celled organisms also evolved from the same single-celled ancestor.  In no evolutionary sense is modern multicellular life more evolved than modern single celled organisms. You can, of course, defined notions of complexity to make multicellular life more complex than single celled life, but such definitions have no evolutionary significance.

We can, of course, say that organisms evolved from earlier organisms.  So the second issue your question brings up is have scientists seen large evolutionary changes in a laboratory setting.  The example you bring up is whether we could observe the evolution of photosynthesis in a lab.

The short answer is no.  We would not expect traits which took millions of years to evolve to evolve in a lab in a shorter amount of time.  In the case of photosynthesis, we may not even have a good idea what selective pressures were involved early in the evolution of cyanobacteria.  Such traits do not usually evolve in their totality in one step.  Instead there are many steps along the way, each of which may be selected for in particular environments for different reasons.  Even if we had millions of years and a very large lab, we may not know of these early selective pressures to successfully recreate the evolution of a particular trait. (There's actually a bit more depth here which I am glossing over. Since the variation in the population is different, the same series of selective pressures won't necessarily yield the same outcome.  When traits evolve through convergent evolution, which is what you are suggesting, they virtually always have different genetic bases and underlying biochemistry.  But a digression into this is probably a distraction from the central point.)

So, you may reasonably ask, if we can not directly observe the evolution of these major traits in a lab, how do we know that they evolved?  There are multiple lines of evidence:

We can see smaller changes occur in shorter periods of time, so it seems likely that the same process creates larger changes in longer periods of time.
For many large traits, we see evidence of common ancestry and the same underlying biology being used for different purposes.
For some traits, we have the evolutionary history of that trait and can identify the sequence of events which brought that trait about (the best evidence generally comes from skeletal traits, where there's preservation).
More speculative evolutionary histories can still be examined through genetic techniques such as molecular clocks, which can indicate when species diverged from a common ancestor.


How many human proteins are very well characterized? Following up on How many human proteins have a solved 3D structure?,is there a list of very well characterized human proteins / protein complexes?

My criteria for "very well characterized" includes, at least:

a high quality 3D structure
known activity in vivo
known associates in its activities in the cell
kinetics of its activity
regulatory elements for expression
etc..., and
(probably most importantly) a general consensus among experts that it is well described

This list would most likely include such proteins or protein complexes as:

P53,
polymerase alpha, and
the nuclear pore complex,

to name a very small number.

To address your list:

a high quality 3D structure: this you can easily get from PDB, using the answers to the question you linked as starting point. However, it is become increasingly clear that intrinsically unstructured proteins also play important roles in the cell, and for these you won't get a good 3D structure.
known activity in vivo / known associates in its activities in the cell: interaction partners can be found in databases like STRING, although just knowing the partners doesn't mean we understand what's going on :)
kinetics of its activity: I know of no good resource on this one except BRENDA for enzyme kinetics. But of course there are also kinetics to protein–protein interactions that would be interesting to know. (Update: There is AffinDB.)
regulatory elements for expression: there are databases like TransFac, but ChIP-Seq experiments show that we only know a tiny part of the regulation.

But, I think the key to a good answer lies here:

  (probably most importantly) a general consensus among experts that it is well described

I would check how often the genes are described in the literature. The GeneRIFs from NCBI may be a good starting point, because these are snippets from the literature that are curated and shown on the NCBI Gene pages. E.g. p53 has >3800 of these. The length of the summary could also be a good proxy. (Or, the length of the Wikipedia page?)


Start studying mathematical biology from basics I am really passionate about theoretical and quantitative biology and I would like to build my future career around this topic.

I've just got my bachelor's degree in biology (ecology) but scince I've had only one math class through the years, my math skills are very poor, so I have problems in understanding even simpe models. My main interests are population dynamics, adaptive dynamics and game theoretical models of social conflicts.

I would like to improve my skills, but I have just no idea where/how to start. Could you give me some advice about textbooks or online resources?

I have almost no knowledge in the field of math, I am interested in resources for complete beginners. And I would also appreciate any suggestions about skills/topics I should master if I am interested in these biological phenomena.

Thank you!

There is one book that will perfectly suits your needs:

A biologist's guide to Mathematical Modeling in Ecology and Evolution, by Sally Otto

It is a very good book that is very easy to understand and in the meantime goes pretty far (It ends with the use of diffusion equation in Evolutionary Biology). I highly recommend it.

It covers:

How to create a model
Function approximation
Find general solution with $n$ variables for discrete and continuous model
Stability analysis
Find equilibrium
Analyzing cyclic behavior
Gives very good introduction in linear algebra and probability theory
Class structured population
Stochastic modeling (birth-death processes and diffusion approximations)
Transformations
All examples are from the field of ecology and evolution and the author derives many of the most important equations in ecology and evolution.

Online ressources

Also I think that Khan Academy is a very good and easy source of information for improving your math skills but it takes quite a bit of time to go through all these lectures.

For a good and complete introduction to probability theory, I'd recommend this MIT Opencourseware but again, it takes time to go through all these videos.

For further recommendations in population genetics, you should have a look to this post.

If you are interested in theoretical biology, you may also want to learn about programming (if you don't already know much about it). $R$ is used for data analysis purposes, $Mathematica$ or $Matlab$ for deal with mathematical modeling and $Python$, $Java$ or $C++$ for individual-based simulations.

Note: A bit less than 2 years ago, I had the same interests than you and had to face the same issues than you.


What does Ercc1-/- / DAT-Cre+ mean? I really need to know what Ercc1-/- / DAT-Cre+  mean. I think the 1st part means that the mice don't have the Ercc1 gene (knockout). But what about DAT-Cre+?

This question arised from reading the following paper: "Inefficient DNA Repair Is an Aging-Related Modifier of Parkinson’s Disease" (Sara Sepe et al).

Ercc1-/- / DAT-Cre+ mice are mentioned several times, For e.g.:

  Ercc1−/−DAT-Cre+ mice are viable and normal at birth. At 26 weeks of
  age, specific deletion of Ercc1 in DA neurons mice elicits reduction
  in tyrosine hydroxylase (TH) immunoreactivity in the SNpc and in the
  striatum (Figures 1A and 1B). Aging profoundly exacerbates SNpc DA
  neurons reduction, as evidenced in 52-week-old Ercc1−/−DAT-Cre+ mice
  (Figure 1C). Damage is limited in DA neurons and other populations
  remain unaffected, as indicated by unchanged NeuN immunoreactivity
  (Figures 1A and 1B). Overall, these findings demonstrate that Ercc1
  function and NER are essential to preserve integrity of the DA
  circuits in time.

Ercc1-/-DAT-Cre means the mice with Cre recombinase mediated conditional knockout of Ercc1 in the DA neurons. DAT-Cre is the mouse strain that expresses Cre recombinase from the promoter of Dopamine transporter.

  Cre-recombinase:loxP (Cre-loxP) system was used to generate mutants
  with targeted deletion in dopamine transporter (DAT)-expressing
  neurons. Specificity of Cre recombinase activity was validated using a
  lacZ reporter that confirmed expression in DA neurons of the SNpc and
  not in other cell types, such as serotonergic neurons of the Raphe
  nucleus (Figure S1).

From supplementary information:

  Conditional mutants were generated using the Cre-recombinase:loxP
  (Cre-loxP) system and crossing a strain carrying an Ercc1 allele
  flanked by loxP sites (Ercc1fl/fl), with a strain expressing the Cre
  recombinase under the control of the specific Dopamine Transporter
  (DAT) promoter (Zhuang et al., 2005). We validated the specificity of
  Cre recombinase activity by generating DAT-Cre+ROSA26-lacZ reporter
  (Soriano, 1999), which confirmed expression in DA neurons of the SNpc
  and not in other cell types, such as serotonergic neurons of the Raphe
  nucleus (Supp. fig. 1)


Phylogenetic Independent Contrasts with discrete traits I understand that PICs are normally only used for continuous traits. However, on this how-to site (https://www.r-phylo.org/wiki/HowTo/Phylogenetic_Independent_Contrasts) there is mention of "Discrete traits can be coded as continuous variables (see ?contr.treatment) and analysed as usual, if they are independent (explanatory) variables."

However, I'm having trouble understanding the commands described in ?contr.treatment and how they relate at all to using discrete traits in PICs. I assume it is a way to transform discrete into continuous data (or at least the appearance of cont. data) so as to perform the PIC, but I don't know how to get there from that hint.

This would very much help analyze my data, which includes both continuous and discrete data. I've already performed a phylogenetic logistic regression, but I feel that PICs could help cement my case if possible to perform.

Assuming that by "discrete", you mean "discrete and ordinal" (like 2, 21, 7, 12) and not "discrete and nominal" (like red, blue, yellow, green), then it is really easy. It just mean you can just use your numbers. The contrast between lineage with average trait 6 and lineage with average trait 9, the contrast is therefore 3.

If your data are nominal, then there is no way to calculate a contrast.

Not however, that typically you might violate assumptions of the PIC model. Make sure to know those assumptions and have a feel of whether you seem to respect them.


Does a mydriatic drug neutralize the action of a miotic? If a person were administered a mydriatic, would the subsequent application of a miotic neutralize the action of the former? If the sequence were reversed would a mydriatic neutralize the effect of a miotic?

The iris has 2 sets of muscles:

The circular muscle (Sphincter iris) - This causes iris constriction and is supplied by the parasympathetic system - Acetyl Choline muscarinic receptors
The radial dilator muscle - This causes dilation of the iris and is supplied by the sympathetic system - The Adrenergic receptors (Alpha 1)

Theoretically speaking, there can be four sets of drugs:

Alpha 1 adrenergic stimulators - will cause midriasis
Alpha 1 adrenergic blockers/antagonists - will cause miosis
Muscarinic blockers - will cause midriasis
Muscarinic agonists/stimulators - will cause miosis

In practice,

Midriatics:

Alpha 1 agonists: Phenylephrine
Muscarinic antagonists: Atropine, Homatropine, cyclopentolate, tropicamide

Miotics (mainly used for Glaucoma):

Muscarinic agonists: Pilocarpine, carbachol, etc...
In practice alpha 1 antagonists are not usually used to effect miosis

There are two ways to achieve either midriasis:

Stimulate the Adrenergic receptors
Inhibit the Muscarinic receptors

Similarly miosis can also be achieved vice-versa.

The answer to your question is yes, when given the proper counter-acting agent, depending on the concentration of the agents and the mechanism of actions opposite effects are achieved. This is primarily because the drugs act on different sets of muscles. If a adrenergic stimulator - phenylephrine is instilled with a muscarinic stimulator - cyclopentolate, both sets of muscles will be acted upon and based on the concentration of the drugs, the decay rate and the efficacy, the iris diameter will either increase or decrease to variable degree. The point is that both the drugs will affect the final diameter of the iris (which is based on the autonomic state of the patient and the strength of drugs administered)

Now the special cases will be to administer a inhibitor of a receptor followed by an stimulator of the same receptor or vice-versa - In this scenario, the duration of action and the affinity of the given drugs to the receptor in question will play a decided role in determining the final action as both drugs act on the same muscle. If the inhibition is permanent or long-acting then inhibition of the muscle action is predominant. This may change if the stimulator has a very high affinity to the receptor - Higher affinity will result in tighter binding of stimulator and remove the chance for the inhibitor to work - i.e. increase the probability of the clearance of inhibitor. As you can see from above statement, if the clearance rate of inhibitor is slow (takes too long to metabolize), then the effect will ultimately be inhibitory effect. Similarly in case of poisonings where the stimulating effect is permanently achieved (Organo Phosphorous poisoning will cause permanent damage to acetylcholinestrase the enzyme responsible to remove acetyl choline) the reversal will depend on the affinity of the inhibitors (in this case, of acetyl choline) to the receptors (muscarinic).

Thus the question must be more specific to get a proper answer, as the effect is totally dependent on the drugs administered.


What is the insight of Frank Starling law of the heart? The Frank Starling law appears to be a trivial observation:

stroke volume is directly related to the end diastolic volume

In everyday language, as more blood fills the heart, the heart pumps more blood out.

Can someone point out whether there are some inaccuracies in the above description because I don't understand why every article on FS law requires upward 20 pages. Even youtube video on this topic is 8 minutes long.

What is the big idea here that I am missing?

This is the short answer from wikipedia :) :

  As the heart fills with more blood than usual, the force of cardiac
  muscular contractions increases.[2] This is a result of an increase in
  the load experienced by each muscle fiber due to the extra blood load
  entering the heart. The stretching of the muscle fibers augments
  cardiac muscle contraction by increasing the calcium sensitivity of
  the myofibrils, [3] causing a greater number of actin-myosin
  cross-bridges to form within the muscle fibers. The force that any
  single cardiac muscle fiber generates is proportional to the initial
  sarcomere length (known as preload), and the stretch on the individual
  fibers is related to the end-diastolic volume of the left and right
  ventricles.

  In the human heart, maximal force is generated with an initial
  sarcomere length of 2.2 micrometers, a length which is rarely exceeded
  in the normal heart. Initial lengths larger or smaller than this
  optimal value will decrease the force the muscle can achieve. For
  larger sarcomere lengths, this is the result of less overlap of the
  thin and thick filaments; for smaller sarcomere lengths, the cause is
  the decreased sensitivity for calcium by the myofilaments.

in one sentence, it is a response to tension.


What is the difference between contig- and read-based sequence alignment? I am trying to understand the difference between read based and contig based alignment. Is contig based alignment refer to de novo assembly and then it is align to a reference genome. I am confused that if you have read based alignment then what is the importance of aligning contigs on the reference.

I have never heard the term “contig based alignment”, and your question is the only Google hit of this exact query (apart from a 2012 patent application).

That said, and without knowing the exact context, I am assuming that you are essentially right: contig-based alignment probably refers to the de novo assembly of reads into contigs, which are then aligned into a scaffold by use of a reference.


How does the age of a parent affect the chances of occurrence of certain genetically transmitted diseases? Do genetically transmitted age-related diseases (like hypertension, arthritis etc.)have the probability of occurring at an earlier(younger) age in the offspring if they are born at a later age to their parent(s)?

In some studies, they have observed either positive or negative association between maternal or paternal age (the age of mother or father at the time of delivery) and earlier development of genetically predisposed diseases, such as diabetes type 1 and certain cancers, in offspring.

Diabetes type 1

Maternal age and diabetes in childhood (BMJ, 2010):

  ...the risk of childhood onset diabetes [type 1] increases with
  maternal age: 5% for each five years of age...the main explanations
  are that biological programming of the child is in some way affected
  by the age of the mother, or perhaps the father...

Cancer

Parental age and risk of sporadic and familial cancer in offspring: implications for germ cell mutagenesis (Epidemiology, 1999)

  We used the nationwide Swedish Family-Cancer Database to analyze the
  effect of parental age on cancer in offspring at ages 15-53
  years...Maternal age was associated with sporadic melanoma and
  leukemia, causing a 30% excess if mothers were more than 40 years vs.
  less than 20 years of age. A marginal effect of about 10% of both
  maternal and paternal age was observed for sporadic breast cancer.

  Paternal age increased the RR of sporadic nervous system cancer by about 15%. Accumulation of chromosomal aberrations and mutations
  during the maturation of germ cells may be a mechanism for these
  findings. In familial cancers of colon, melanoma, and thyroid, higher
  age showed an apparent protective effect, which was also noted for
  sporadic cervical cancer and melanoma.

Rheumatoid arthritis

Ages of onset suggestive of genetic anticipation in rheumatoid arthritis multicase sibships can be explained by observational bias (Rheumatology, 2007)

  There was no significant correlation between the age of RA onset and
  the maternal or paternal ages of conception.

Cardiovascular disease

In one study, they have found no significant association between maternal age and blood pressure in children. There seem to be no studies about the effect of maternal/paternal age on early-onset heart disease.

On the other hand, offsprings are at increased risk of developing a cardiovascular disease early if their parents had it early (PLoS One, 2016).

In another study, they have observed that maternal ages <25 and >45 have been associated with increased frailty index: a sum of 8 conditions (cancer, lung disease, mental health problems, diabetes, heart disease, stroke, blood pressure and arthritis)

Maternal Age and Offspring Adult Health: Evidence From the Health and Retirement Study (Demography, 2012)

  In summary, net of some obvious confounders, only maternal ages below
  25 and above 45 are associated with negative offspring health
  outcomes. (see Fig 1 and Table 2)

  The mechanisms thought to be responsible for the young maternal
  age–offspring health link are related to the physiological immaturity
  and sociodemographic disadvantage that often accompany young
  parenthood... On the other hand, the negative association between advanced
  maternal age and adult health is thought to be driven by the
  physiological reproductive aging of the mother.

In this study, they have not checked for the age of onset of diseases in offspring, though.


Why is PCR possible to amplify DNA template before Sanger Sequencing for unknown DNA sequences? Most of the informations show that both PCR and cloning can be used before Sanger Sequencing to amplify the DNA template. But how is it possible for us to design the primers if we don't know the DNA sequence yet? So, in my opinion, only cloning is possible to amplify the sequences. Can anyone tell me how PCR can work in this way? Thank you!

PCR is used to amplify a sequence included inside two known regions. So, if you're able to clone (for example with recombination) two sequence forward and backward to your sequence, by using PCR you'll amplify also the sequence included.

This image in example will clarify my statement.


Role of isopropanol in plasmid isolation In plasmid isolation, isopropanol is used to renature only the plasmid macromolecules after we precipitate all macromolecules(DNA, RNA, plasmids) using sodium acetate solution. How does it do that? How does it not renature every other macromolecule?

In a standard DNA preparatory procedure, isopropanol is used to precipitate the DNA. Nucleic acids are insoluble in alcohols, and bulk or stick together. This sticking together can be further enhanced by increasing the ionic strength such as through addition of sodium acetate.

alcohols in fact don't really denature the DNA.


Why do dragonflies have these special little spots on their wings? The wings of several kinds of dragonflies I've seen here in Taiwan all have an apparently special little pigmented spot near the ends of each wing.
Does this spot have a name and a function?
below x2: Taken today in Hsinchu county, Taiwan. Note arrows. I've also asked Identify these two large dragonflies in Taiwan?
Click for full size

below left: from Identify this black dragonfly with bluish coloration along its flat top, yellow on it's mid-body and green on its head  below right: from Identify this black dragonfly with a bright bluish-white band around its body
Click for full size

Pterostigma is what those spots are. Wikipedia article is at https://en.wikipedia.org/wiki/Pterostigma.
I read the summary of the technical article below.
The pterostigma are heavier than the rest if the wing, and so the insect can glide faster without a destabilising flutter beginning.
The author also believes that the pterostigma contribute to more efficient active flight.
Technical details at:
Norberg, R. Åke. "The pterostigma of insect wings an inertial regulator of wing pitch". Journal of Comparative Physiology A. 81 (1): 9–22.
doi:10.1007/BF00693547.


Will a person with two copies of the same set of chromosomes be normal? Would a (theoretical) woman (because she must have two X's), that both sets of
her chromosomes were 100% identical, be "normal"?

Would she be healthy, or would she have genetic problems as a result of that?

Would all her egg cells contain the same copy, identical to all others in her
body?

Thanks very much for any answers!

It sounds like this person would be close to what you get with "pure lines", aka inbred strains in laboratory animals:

  A population of identical homozygotes constitutes a pure line. Pure lines "breed true"; that is, they maintain their phenotype indefinitely if genetic crosses are restricted to members of the pure line (see True Breeding).

You get those by inbreeding for enough generations that the individuals become genetically identical, or monozygous for every allele at least.

And on the effect of being a homozygote for all genes:

  Inbreeding in allogamic organisms bring the deleterious recessive alleles to homozygosity; the immediate consequence is an increase in the frequency of defective offspring, or, in another words, an increase in the genetic load of the population. This phenomenon is called inbreeding depression or inbreeding degeneration. As inbreeding continues, the deleterious alleles are selected out and eventually disappear.  The original heterozygous populations are often more fit than the resulting pure lines because they profit from heterosis and balanced polymorphisms; the main advantage of pure lines is the quick production of many individuals with the same well-adapted genotype

It sounds like she would only have genetic problems if she had problem genes; bad alleles are more likely to be harmful if you're monozygotic for them because there are no other alleles to compensate, but if you only have the good alleles to begin with there's no harm. You would have problems in cases where having two different alleles is itself superior to having a single one of any; for things like immunity for example that can be the case. Or being heterozygous for the sickle-cell allele in malaria country, for another standard example.

I don't know if any of those things would be harmful enough that we'd call that woman "unhealthy" or "suffering from genetic problems" though. I think if it did, it would be more a statement about how the human genomes contains these specific alleles that you have to be heterozygous for than about the intrinsic harm of being the combination of two identical haploid genomes.

As for whether her egg cells would all be identical, they should be since homologous recombination should be switching identical bits of DNA with each other, but that's ignoring mutations. Which shouldn't be ignored, because every human has on the order of 100 mutations that weren't in their parents. Still, compared to how much DNA there is in the eggs overall it would also be reasonable to call them identical.


What is the energy consumption of the brain? What is the energy consumption of the brain, and is there a difference in consumption when waking and sleeping?

I assume that you mean energy consumption.

Talking in round numbers the daily energy requirement of a sedentary human is 2,500 kcal. It's usually said that the brain uses 20% of this energy.

What does this mean in terms of power consumption?

500 kcal = 500 x 1000 x 4.2 J  -[1]
24 h = 24 x 60 x 60 s          -[2]

1 W = 1 J/s

therefore brain power  = [1]/[2] = approximately 24 W

Most of the energy consumed by the brain is used in maintaining membrane potentials so energy is used continuously. I would think that there will be very little difference between waking and sleeping.


Is there any biological reason for humans to rest after x days of work? A lot of people live in a 7 day cycle, where 5 days of work are followed by 2 days of "rest". Vacations and holidays can increase the time available for resting.

Is there any biological reason for humans to rest after x days of work? Can this be explained by the buildup of by-products of metabolism, like Homocysteine?

I think your main assumption is not true -- we do not really rest on weekends.

I do not know many people who only rest on weekends. Usually this is the time for socializing, doing home-related work, physical activity (sports, hiking), spending time with your kids, all of which is often almost the opposite of a rest.


Why does inbreed produce a higher percentage of abnormal babies? The babies of close (say, brother and sister, or cousin and niece) family members have a higher chance of being born with an abnormality than babies from non-family related men and women. Why?

Many disease/abnormality causing alleles of a genes are maintained in populations through their recessive nature. That is to say, in order for the disease to manifest itself in offspring they must in have TWO copies of the disease causing allele - they must be homozygous for the disease causing allele. Inbreeding leads to a far greater chance of being homozygous at a disease locus if a recent common ancestor of the parents was affected or a carrier. The likelihood of this occurring is measured by the Inbreeding Coefficient.


Electron balance for biomass synthesis: is my professor right? I'm studying for my exam and I came across these notes written by the professor himself. He's talking about the general reaction of biomass production in a bioreactor:

$$\ce{C6H12O6 + NH4+ + O2 -> $\mathrm{C_wH_xO_yN_z}$ + CO2 + H2O + H+}
\\\text{(not balanced)}$$

At some point he proceeds to do the "reduction balance" for this reaction: he calculates the "reduction degree" of the elements (which he defines the same way I define the oxidation number) and here comes the problem.

He states the "reduction degree" of C in glucose is +4 and the one of O in O2 is -2.

Is "reduction degree" different from oxidation number? Are there any particular ways to calculate oxidation numbers when you talk about biomass?

Thank you for your help.

The terms are different.
Oxidation number is the difference in number of electrons (not pairs) from the elemental form (which for many elements exists only on paper) of an atom.
Degree of reduction is a more uncommon term that is basically the number of electrons that atoms in a molecule are donating per atoms of a given element. It is calculated formally by summing the number of electrons donated to reach a full shell (H=1, C=4, N=-3, O=-2, P=5, S=6 etc.) divided by the number of a given element, but that is more confusing than anything.
Carbon can be oxidised four times, e.g. methane > methanol > formaldehyde > formate > carbon dioxide (not biological route, just an example), while oxygen can be reduced twice: to hydrogen peroxide and then to water. As proof, most O2 dependent enzymes produce hydrogen peroxide (e.g. FADH2 enzymes). That is a cheat way to work out where those numbers come from.
I would recommend forgetting about the formal calculations of oxidation numbers —in biology oxidation numbers of carbon are generally not discussed.
I will open the brief parenthesis of the oxidation states of carbon just to point out they are not those: -1 for a bond with hydrogen, +1 with oxygen and 0 for a C-C bond. Carbon monoxide therefore has an oxidation state of +4, while a C in glucose (on average) has a -1. Molecular oxygen has two identical atoms therefore is 0. Elemental carbon has 6 electrons so hypothetically you cannot strip carbon more than +6.
Here what is important is figuring out how many times a carbon in a molecule can be oxidised, that is how many electron pairs a molecule can give away as every time that happens an NAD+ (catabolism) or NADP+ (anabolism) is reduced, which is key to the cell. A dehydratase removes a hydroxyl group leaving an alkene, but it does not carry out a redox reaction: the geometry is no longer sp3, but sp2, and the oxidation state has decrease by 1 in that carbon, yet carbon kept its electrons —the other carbon increased by 1 as it deprotonated, so no net change and NADH is not generated.
Knowing how many electron pairs are given away going from glucose to carbon dioxide is important because cells cannot make them disappear and a terminal electron acceptor is needed either in the form of respiration or fermentation. There is a further concept, that of reduction potential. Different forms of terminal electron acceptors are employed in Nature: oxygen, Fe(III), sulfate etc. and these have different "energy" levels at which they accept the electrons (reduction potential, measured in volts), which translated to different amounts of energy that can be syphoned off during the reaction.


What about a bat's immune system protects them from Ebola? Current evidence indicates that fruit bats are a reservoir host for Ebola. Has any research established what is different about their cell biology or immune system that reduces virulence for them?
Failing research on this particular system, do you have an example in another system of how virulence is reduced in the reservoir host?

I'm teaching a cell biology class, so actual examples of modified proteins or enzymes or inflammatory molecules in the reservoir is preferred.

The main reason for this is that fruit bats are most likely (I don't think there has been a direct proof for Ebola so far) the reservoir host for this disease. The reservoir host is adapted to the disease and can harbour it for an indefinite time (with recurring infections) without showing signs of an infection or being affected by it. Although it is not getting sick, the reservoir host can pass the disease to other animals.

There is very little known about the immune system of bats, but they seem to be different, so they are not affected by diseases which cause havoc in humans. The following papers go into some details and they are interesting to read:

Bats: Important Reservoir Hosts of Emerging Viruses
Bats and their virome: an important source of emerging viruses
capable of infecting humans.

These papers give an interesting view of the bats immune system. The first article is a short explanation of the most important findings of the second. It looks into differences between species and analyse how the bats immune system may have evolved. Really interesting.

Of bats, flight and immunity to viruses
Comparative analysis of bat genomes provides insight into the
evolution of flight and immunity.
Antiviral Immune Responses of Bats: A Review


What is the name of this plant? This plant was found growing in Germany. I have never seen it before, reverse Google image search did not help either. Can you help me identify what type of plant this is?

Thanks, looks like it is something like this:

http://pflanzen-enzyklopaedie.eu/stauden/amerikanische-kermesbeere-phytolacca-americana/#more-4034

Related question:

https://gardening.stackexchange.com/questions/2609/what-is-this-fast-growing-plant-with-blue-black-berries/2610#2610

This looks like some species of Phytolacca to me.

It's possibly Phytolacca americana, which is native to the US (in fact it's an enthusiastic 'volunteer' in my garden) but naturalized in Europe.

If you still have any in the ground, once they ripen, the berries are intensely purple and can be used as dye (or even eaten?)

Mark A. Nienaber & John W. Thieret. Phytolaccaceae.  In: Flora of North America Editorial Committee, eds.  1993+.  Flora of North America North of Mexico. New York and Oxford. (link goes to entry of P. americana)


How can I preserve hair or saliva for future genome sequencing? Suppose I want to preserve myself so that I can be reproduced as best as possible, in future or be simulated in future. At the moment full human genome sequencing is a bit expensive.

One could get some of my hair or saliva, but what can I do with it to best preserve it?

Would it need to be put in a freezer?

How long would the DNA of the hair or saliva be preserved for in a regular kitchen freezer?

How long would the DNA be preserved if the hair or saliva was not in a freezer?

Are there any issues of contamination?

Also, once the full genome sequencing has been done, is that all the info that could be gleaned from it genetically? can the hair/saliva be thrown out, or might it be possible that future human genome sequencing could pull more info from the sample?

Full genome sequencing is only one of many experimental approaches. It's important in the field of genomics and useful in transcriptomics and proteomics.

It's best to extract DNA as soon as the sample has been removed from the living organism since all kinds of physiological processes start breaking down DNA in dead tissue. Kitchen refrigerators are not ideal for storing extracted DNA because they operate at about four degrees celsius. In the lab, minus eighty degree freezers are used. The lower the temperature, the better. Minus eighty degrees, however, is good enough.

Contamination is a big problem, so the more technical repeats you run, and the more biological repeats you have, the better your chances of getting reliable results. Biological repeats refer to, for example, taking three strands of your hair for analysis, while technical repeats refer to, for example, carrying out three PCR experiments on material from the same strand of hair. Once you've used tissue to extract DNA you don't keep remaining tissue because it gets contaminated during experimental preparation. That is why you may want to have biological repeats. It's also important to take precaution when removing the sample from the organism. This means wearing latex gloves and even using dilute ethanol to sterilize the sample before placing it in a sterile container. The problem is that ethanol can interfere with DNA extraction and be a contaminant itself. Balancing contamination prevention with quality results is important in the lab.

There are additional biological information such as DNA methylation events that occur intermittently on a genome and are inheritable. This information cannot be predicted from the sequence composition of your genome, but there are experiments meant for elucidating methylation patterns that can be carried out using uncontaminated biological samples (such as hair and saliva) stored in eppendorf tubes at minus eighty degrees celsius.


What is the role of pyrophosphatase in RNA polymerization? In Molecular Cell Biology (8th edition) there's a fragment in chapter 5.2 that says:

The energetics of the polymerization reaction strongly favor the addition of ribonucleotides to the growing RNA chain because the high-energy bond between the α and β phosphates of rNTP monomers is replaced by the lower-energy phosphodiester bond between nucleotides. The equilibrium for the reaction is driven further toward chain elongation by pyrophosphatase, an enzyme that catalyzes cleavage of the released PPi into two molecules of inorganic phosphate.

How does the pyrophosphatase make the reaction more favorable? Does it make "harder" for triphosphates to form back again (now you have to attach phosphates one by one, not two at once)? If so, isn't one additional phosphate just as bad as two? To remove either you have to break one bond (between the first phosphate and the second), and you have a specialized enzyme to remove two of them (the RNA polymerase). Isn't forming a diphosphate (which needs to form in order to later make triphosphate) actually worse? Or maybe it somehow "reuses" energy stored in the bond between the two phosphates left?
Sorry if I didn't use the proper vocabulary, I'm new to biology.

This question can be answered by considerations of chemical equilibrium. For any chemical reaction:
$$\ce{A + B <=> C + D}$$
It is a property of nature that removal of product ($C$ or $D$) from the reaction mixture drives the reaction in the forward direction. This is an example of le Chatelier's principle and can be explained as follows:
In a reaction mixture containing $A$, $B$, $C$ and $D$, the rate of forward reaction ($A + B \rightarrow C + D$) depends on the frequency of collision of $A$ and $B$ molecules. Similarly, the rate of backward reaction ($C + D \rightarrow A + B$) depends on the rate of collision of $C$ and $D$ molecules. The collision frequencies, in turn, increase with concentration of the relevant species. An abrupt reduction in the concentration of $C$ hinders the backward reaction while leaving the forward reaction unchanged. Thus the forward reaction begins to dominate.
The reaction catalysed by RNA polymerase is:
$$\ce{RNA + NTP <=> Longer \ RNA + PP_i}$$
By removing $\text{PP}_i$ from the reaction mixture, pyrophosphatase does exactly that and drives the reaction in favour of RNA polymerisation. Note that hydrolysis of pyrophosphate is favoured because of the negative free energy change associated with it (thanks to David for pointing that out).


Is this plant with very asymmetric leafes Aegopodium podagraria (aka ground elder)? I found this plant in a city park in Germany. The leaves were about 20cm of height; the smell of the squeezed leaves was a bit like carrots. The stems were edged. So I guess it was Aegopodium podagraria (aka ground elder), but I'm not sure about it.

A man, collecting herbs, confirmed my suggestion about Aegopodium podagraria. Together with what I read about this plant, I can set my question as being answered with Yes.


How to predict a mRNA secondary structure with a large sequence? When I use some web servers to predict a mRNA secondary structure, I find they always required in a small size sequence. If I use a long sequence and cut it into small parts, do these small parts change the energy or thermodynamic data from the origin sequence when predicting? Is there any effective way to find the right sites when cutting the long sequence?

Yes, the structure predicted by splitting up the sequence may not represent the actual structure of the full-length RNA. A simple hypothetical case would be that of an RNA whose 3' and 5' UTR interact to cause circularization.

I am afraid there is not clear rule for choosing the subsequences such that the assembly of the individual secondary structures is closest the the actual structure.

We may expect that, with better computational power, the limitation on the size of the sequence for secondary structure prediction, can be overcome.

However, there are experimental techniques using RNA-sequencing that can determine the actual secondary structure — SHAPE-seq (ver 2.0; Loughrey et al. 2014) and structure-seq (Ding et al. 2014). Structure-seq in-fact, tries to determine the RNA secondary structures in-vivo and hence may be a more powerful tool.

However, you said you are working with mRNAs. I guess for mRNAs you can predict the structures of UTRs and the CDS separately. Actually depends on what you are interested in. CDS usually does not harbour any structural motif and any secondary structure in the CDS is usually resolved by the helicase activity of eIF4A. However, secondary structures can slow down the translation elongation rate (Mao et al. 2010, Gorochowski et al. 2015).

Loughrey, D., Watters, K. E., Settle, A. H., & Lucks, J. B. (2014). SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing. Nucleic acids research, 42(21) e165.
Ding, Y., Tang, Y., Kwok, C. K., Zhang, Y., Bevilacqua, P. C., & Assmann, S. M. (2014). In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature, 505(7485), 696-700.
Mao, Y., Liu, H., Liu, Y., & Tao, S. (2014). Deciphering the rules by which dynamics of mRNA secondary structure affect translation efficiency in Saccharomyces cerevisiae. Nucleic acids research, 42(8), 4813-4822.
Gorochowski, T. E., Ignatova, Z., Bovenberg, R. A., & Roubos, J. A. (2015). Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate. Nucleic acids research, gkv199.


What is this white, winged insect? I saw this insect crawling on a wall in the UK (Birmingham) today (March 28th). It's about 5mm long. I assumed it was a white fly, but having looked at other images of white files on google, I don't think it is! I assume the fact it has jet black eyes means it's normally nocturnal?

At first I was thinking Trichoptera, but the antenna were not long enough and I noticed your size is quite small (~5mm).

The small size and body stance made me think of the order Neuroptera (the net-winged insects).

Specifically, this specimen reminds me of the family Coniopterygidae (or the dustywings).

  A distinguishing feature is that like many other Neuroptera, dustywings carry their wings nearly side-by-side when at rest, whereas whiteflies carry them almost flat across the back  [the last part being related to the OP's original thought that their specimen was a whitefly]

Interestingly, unlike many other net-winged insects, the dustywings do not actually have "net-winged" venation -- just like the OP's specimen.

If this is in fact a dustywing, according to Wikipedia:

  These tiny insects can usually be determined to genus with a hand lens according to their wing venation, but to distinguish species, examination of the genitals by microscope is usually necessary.

Just as a reference, according to here and here, a similar looking species called Conwentzia pineticola lives in the UK. You can see a picture of this species below:

 Source: NatureSpot

Comments on appearance and characteristics:

From Catherine A. Tauber et al. (2009) in Encyclopedia of Insects (Second Edition):

  The Coniopterygidae is generally a very homogeneous family characterized by very small adults (forewing length 2–5 mm) with bodies covered by white waxy (“dusty”) secretions.

The family name means "dusty wing" [source] due to the usually conspicuous whitish dust of waxy scales on the wings of these insects. I can't tell if this "dusty" nature is apparent in your picture or whether your picture is simply blurry.

Regarding the antenna, Tauber et al mention:

  Adults have chewing mouthparts, large compound eyes located laterally on the head, and multiarticulate antennae that are usually filiform (thread-like) or moniliform (with bead-like segments).

You can see a similar looking (and similar sized) specimen from the U.S. here and one from Spain here. Additional images on bugguide.net seem to suggest that your specimen is in the subfamily Coniopteryginae.


What are the effects of oxygen toxicity in human blood? I was reading some text on deep sea Physiology, and for to know that diving to do could cause oxygen toxicity in the blood. This was the exact text from the book Textbook of Medical Physiology by Arthur Guyton and John E. Hall:

A  column  of seawater  33  feet  (10.1  meters)  deep  exerts  the  same  pressure  at  its  bottom  as  the  pressure  of  the  atmosphere  above the  sea.  Therefore,  a  person  33  feet  beneath  the  ocean surface  is  exposed  to  2  atmospheres  pressure,  with  1  atmosphere  of  pressure  caused  by  the  weight  of  the  air  above the  water  and  the  second  atmosphere caused by the weight of  the  water.
When  the  PO2  in  the  blood  rises  above  100  mm  Hg, the  amount  of  O2  dissolved  in  the  water  of  the  blood increases  markedly. Note  that in  the  normal  range  of  alveolar  PO2  (below  120  mm  Hg), almost  none  of  the  total  O2  in  the  blood  is  accounted  for by  dissolved  O2,  but  as  the  O2  pressure  rises  into  the thousands  of  millimeters  of  mercury,  a  large  portion  of the  total  O2  is  then  dissolved  in  the  water  of  the  blood,  in addition  to  that  bound  with  hemoglobin.

I understand that high pressure causes more oxygen to dissolve in blood, but cannot figure out how excess dissolved oxygen in the blood disturbs the normal physiological balance of the body.
I'd be grateful if someone knowing the answer can help me.

This is from a Wikipedia article:

Central nervous system oxygen toxicity manifests as symptoms such as visual changes (especially tunnel vision), ringing in the ears (tinnitus), nausea, twitching (especially of the face), behavioural changes (irritability, anxiety, confusion), and dizziness.
Oxygen toxicity - Wikipedia
https://en.wikipedia.org/wiki/Oxygen_toxicity

It says there's hemolysis of red blood cells - i.e., they lyse = break open.


How exactly is the wood fossil process? I would like to know in deep how exactly is the wood fossilisation process. I am fascinated how after millions of years the fossil wood preserves its microscopic characteristics. Look at this cross section where you can see clearly differences in the cellular tissues as parenchyma, vessels, and rays.

I know that in the fossilisation process the wood was replaced by mineral particles, but I don't understand how the organic material went outside to stay only the minerals.

there are actually more than one process, but in the case of high detail wood fossils the process is the slow filling in of all the spaces in the wood (filled with water in life) with dissolved minerals from the groundwater. this is called permineralization. Of course this only works is the wood is buried so it cannot rot while this is happening. Since permineralization happens on the molecular level is can preserve great detail as the minerals form around the remaining hard tissue.

This video is a decent representation,


Why do so many people have group O blood? Please forgive me in case my question wouldn't make much sense. I was reading about ABO blood groups on Wikipedia, where I learnt that O is a recessive allele, and that it seems the A allele predates the O allele. My question is, therefore, how is it possible that almost half of the human population is group O?

For instance, I would expect (quite naively I reckon), if only alleles A and O existed, that around 75% of the population should be A, and 25% should be O.

There are many different variants of O (all loss-of-function) indicating that this mutation has arisen many times in the human population. The prevalence of O is indeed taken as evidence of balancing selection. Various pathogens use the A or B antigens as receptors. The cited paper presents evidence about the phylogeny of the ABO gene in human populations and reports that there is clear evidence of balancing selection.

We propose several hypotheses for the cause of [balancing selection], which most likely involved interactions with multiple pathogens at different geographic regions and timescales.
Calafell et al (2008) Evolutionary dynamics of the human ABO gene. Human Genetics 124: 123-135


Difference between "controlled release" vs "prolonged release" My sister is using the epilepsy drug Tegretol which has both CR and retard (previous naming for prolonged release according to https://www.medicines.org.uk/emc/product/5932/smpc) versions in different countries. Given the active ingredient is the same (carbamazepine), would there be any difference between the effects of the two drugs in terms of preventing seizures?

Here are the boxes for the two versions:

The first box contains Tegretol Retard, which is an old name for what is now known as Tegretol Prolonged Release (medicines.org.uk).

The second box contains Tegretol CR, which means controlled-release (PubMed).

Drugs.com says:

  Your medicine is called Tegretol 200mg prolonged-release
  Tablets/Tegretol CR 200mg Tablets or Tegretol 400mg prolonged-release
  Tablets/Tegretol CR 400mg Tablets but will be referred to as Tegretol
  prolonged-release Tablets throughout this leaflet.

Concluding from that, Tegretol CR200 is the same as Tegretol Retard, which is now known as Tegretol Prolonged Release.

Saying that, it is a doctor who prescribes drugs and who can answer such questions.


Passing out from drowning How long does it take to pass out from oxygen deprivation? The person is panicked and screaming so they accidentally breathe water into the lungs. So how long would it take for them to pass out? After they pass out they are administered Mouth-to-mouth resuscitation immediately and are only out of it for a couple of half a minute. Then they are taken to the hospital. Would there be any long term affects to the body?

A couple of half a minute? Anything under 5 minutes is a 90% chance of being safe if resuscitated. Drowning people don't make much noise because they are too distracted by the water. They only fill their lungs significantly after becoming unconscious.

simple description:
https://www.dedhamhealthfoundation.org/water/victim-recognition/stages-of-drowning/

complex description:
https://en.wikipedia.org/wiki/Drowning#Pathophysiology

The damages that occur are: lung injury, cardiac arrest, brain injury from oxygen deprivation.

The breathing pattern and physiology vary depending on hyperventilation, panic, physical exertion, fullness of the lungs at the time of submersion, so there is no simple answer to your query.

When they breathe significant amounts of water, it is because they have just lost consciousness and their body relaxes.

While they are is still conscious, they hold their breath for as long as they can, voluntarily / because they have breathed a sip of water and their epiglottis shuts and seals closed, by reflex.

There is a spasm called laryngospasm which occurs when the person is at the end of their breath and their body is trying to breath but their epiglottis is closed, that occurs at very low oxygen levels and a high oxygen debt because of the panic, so unconsciousness is only a few seconds away when the throat is convulsing, and it continues to convulse when they are unconscious and 90% of the time they breathe water and their heart continues beating.

I can't find how long it takes to have cardiac arrest after asphyxia or wet drowning. Probably it is not very well studied becuase it is so dangerous.

There is also the mammalian dive reflex, which occurs mostly in children who are suddenly immersed in freezing water. It can cause their metabolism and heart rate to go into slow motion, and stops circulation to their extremities, causing them to survive for more than 15-30 minutes.

This is a kayak trip heart rate with immersion in cold water.

From avalanche asphyxia, the heart can continue 15-20 minutes:
https://www.scancrit.com/2013/08/27/heart-rate-monitor-watches-avalanches/

There's a dutch man who lost his wife and then started diving in freezing water, and he can stay in freezing water for 30 minutes using conscious mammalian dive reflex.


Is there any complex organism that is both autotroph and heterotroph? Possibility also include "adaptation mode" if such exist. I don't discern whether autotrophic/heterotrophic part play only minor role either.

For example sundews are plants (so autotrophic), but they "hunt" for insects to get additional nutrients, e.g. nitrogen. As far as I remember the nitrogen is the main reason for eating other organisms but they also use other substances, including carbohydrates, from their prey.


Having a lot of trouble identifying this insect It was found in central Alabama

Other's are right, some genera in the subfamily Reduviinae, I don't think it's an adult though. Very close to this.


Has autogamy been observed in any animals? By my understanding, autogamy, i.e., reproduction that is sexual, but with both gametes contributed by the same individual, is not at all uncommon in the plant kingdom.
Does this also occur anywhere in the animal kingdom?

Yes, there are some animals which are known to self-fertilize (although generally not exclusively).  For instance, among invertebrates some nematodes are known to use self fertilization, as discussed in this paper about its evolution.  Among vertebrates, it seems to be very rare, apparently known only only in a single genus of fish.


How can I find a complete human genome file I'm trying to figure out how I can download a file that represents the complete human DNA sequence. I don't care too much about the format – I'm able to write C++ code to parse it. FASTA seems like a simple format though. What I haven't figured out yet is where I can find a complete file – I have found what appear to be subsets of genes or other sequences or single chromosomes but aren't there 46 chromosomes to include or are some of those duplicates (i.e. 22 chromosomes + 2 sex chromosomes)?

On this page, I have found this list of files under "Human > Genome assembly: GRCh38" but it appears to be broken up by chromosome or something? If so, would I merge these? My goal is to display all the letters via projector onto a wall and I want to be able to point at it and tell someone, that's all the DNA for a human (not a subset). Also, to double check, it is a "genome assembly" I want right? By the way, I don't care about allele variants right now.

Please consider in your response that I am not familiar with much of the lingo, thank you.

The National Centre for Biotechnology Information has a link to a genomes FTP site - on that page, there is a file labelled .../genomes/H_sapiens (this a direct link to that directory).

There are numerous files therein.  From the README file:

  Sequence data include chromosomes, contigs, RNAs, and proteins
  generated through the NCBI Reference Sequence and NCBI Genome
  Annotation projects. Map data presented in the Map Viewer resource are
  also provided here.


How do the lungs act as a sieve to trap blood clots? Does anyone know? I'm curious to find out  as my human anatomy and physiology book doesn't go into much detail on how the lungs function as such

Just as an intro...

The heart pumps deoxygenated blood from the right ventricle, through the pulmonary arteries (pic) which then eventually split into small capillary networks that surround the alveoli. The alveoli are formed by the trachea eventually branching off. So when you breathe in, the alveoli become filled with higher levels of oxygen.

The blood then becomes oxygenated and returns to the heart via the pulmonary veins to be pumped to the rest of the body.

The deoxygenated blood becomes oxygenated because there is a difference in oxygen and carbon dioxide concentration between the capillary network (O2 low / CO2 high) and the alveoli (O2 high / CO2 low) and so gas diffuses across because of the difference in concentrations (pic).

Physiology textbooks explain these mechanisms but for blood clots in particular, you'll need to check out a pathophysiology book.

Blood clots

When a blood clot travels to the lungs, it's referred to as a pulmonary embolus or PE.

Most of the time (90%), pulmonary emboli are formed in deep veins of the lower leg. These then travel to the pulmonary circulation system.

Large emboli block larger vessels - the pulmonary arteries and their branches. The smaller ones travel further into the network.

Patients can sometimes be asymptomatic and the emboli can at times resolve on its own. The extent of the severity of a PE is determined by:

how much blood flow is obstructed;
how long the embolus has been there; and
presence other underlying lung or heart disease.

There are a number of things that a PE can cause physiologically.

Reduced Gas Exchange - alveolar dead space occurs when an alveolus is ventilated, but not perfused with blood. This, along with other factors, cause varying levels of hypoxemia (lack of oxygen).

Pulmonary Infarction - in a small amount of cases loss of blood flow to lung tissue can cause tissue death. This is fairly uncommon.

Right Ventricular Failure - if there is a large enough blockage (> 50 - 60%), the pressure in the pulmonary arteries increase. Subsequently, the load on the right ventricle is higher.
So in acute cases, the ventricle hasn't had time to adapt (hypertrophy) and so the right heart can fail.

At any rate, the haemodynamic balance can be disrupted when a PE is present.

In the elderly or people with underlying disease where their lung function is already decreased, PEs can have a significantly larger effect because they can't compensate. There are many more important points related to this but hopefully this is a useful (very) basic overview.


Meaning of “cognate genes encode the basic biological functions of proteins” In the introduction to a review article entitled “Interpreting the protein language using proteomics” the author uses the term ‘cognate genes’ in a manner which I do not understand:

  Whereas cognate genes encode the basic biological functions of
  proteins, the real-time dynamics and regulation of protein structure
  and function are generally carried out by specific post-translational
  modifications (PTMs) of proteins such as phosphorylation,
  glycosylation and acylation.

What does it mean?

The sentence quoted accidentally misuses the word ‘cognate’ because in attempting to appear profound it has become overweight and off-balance. Notice the sentence also contains the meaningless nonsense of “real-time dynamics”, and in the rest of the paper the word ‘cognate’ is (fortunately) nowhere to be found.

What does the author mean? His review is on proteomics, and he wishes to emphasize the importance of post-translation modification of proteins. He needs to refer to the unmodified form of proteins, and so he associates them with the information in their genes, which is limited to the unmodified amino acids. The word ‘cognate’ in plain English has the meaning of ‘related’ or ‘corresponding’, so the author would appear to be using it to imply the relationship between particular genes and the individual proteins that they encode. What he may have meant to say is:

  “Whereas genes encode the basic biological functions of their
  cognate proteins…”

This would have been linguistically correct, although the word ‘cognate’, in my opinion is unnecessary as it adds nothing to the sentence.

You can find a biological definition of cognate on GenScript:

  cognate

  A term borrowed from linguistics, signifying a correspondence;
  e.g. a receptor and its cognate ligand, a tRNA and its cognate amino
  acid.

These two examples are of the most common uses of ‘cognate’ in molecular biology — that for tRNA can be found on the Wikipedia page for aminoacyl tRNA synthetase. A quick search brought up few examples of ‘cognate proteins’ or ‘cognate genes’, and in these cases I found the word was used to refer to similar genes or proteins in different organisms or strains.


miRNA analysis just using BLAST against mirbase.org I have sequencing data (Illumina). Library prep was focused on short ncRNAs. I would like to identify human miRNAs. Do you think it is feasible to simply BLAST against a current version of mirBase and filter the output for mature, human miRNAs without using bowtie/tophat against hg19 first?

Thanks

You don't need to use TopHat but it is better to use bowtie instead of BLAST. First of all you need to get rid of the adapter sequences (along with other processing steps prior to alignment).

Now there are two aspects here:

miRNA quantification
miRNA discovery

First one is relatively straightforward whereas the second one requires you to perform additional tests such as prediction of stem loops etc. There are published software that can handle both the aspects (mirDeep, miRScan etc). See this review for details on different miRNA gene finders. I have used miRdeep and it uses bowtie-1 to align.

BLAST would work but you have to set parameters which are suitable for small sequences (increase E-value cutoff, reduce word size etc). Moreover, BLAST does not have a cutoff option for the number of mismatches and the length of alignment (it only has a post alignment filter for percentage identity).

I also personally prefer bowtie because it has something called as n- alignment mode. In this mode the entire read is divided into seed and non-seed regions. You can specify the length of the seed region and the mismatch cutoff. Since for miRNAs the seed region (bases 2-8) is critical for its function, I generally set the seed mismatch cutoff to zero while allowing one or two mismatches in the non-seed region (note that in bowtie the seed always starts at 1).

In general, I would advise that you should go for miRdeep instead of BLAST. However, miRdeep doesn't straight away perform an alignment against the mature sequences. It maps the location of mature sequences in the pre-miRNA sequences (stem loops) and then aligns the reads to the pre-miRNA sequences. If the location of reads has a significant overlap with the mature region (you can adjust the window) then the read is considered as a valid miRNA.


How is it thought that phosphine is synthesized by living organisms on Earth? The recent (Sept. 2020) report of “Phosphine gas in the cloud decks of Venus” states that phosphine (PH3) is only known to occur on Earth due to anaerobic life. Quoting from a report in the New York Times:

But scientists have yet to explain how Earth microbes make it.
“There’s not a lot of understanding of where it’s coming from, how it forms, things like that,” said Matthew Pasek, a geoscientist at the University of South Florida in Tampa. “We’ve seen it associated with where microbes are at, but we have not seen a microbe do it, which is a subtle difference, but an important one.”

What are the current hypotheses about how phosphine is formed?

The background to phosphine production on Earth can be found in a review entitled “Natural Products Containing ‘Rare’ Organophosphorus Functional Groups” by Petkowski et al. in Molecules  24, 866 (2019). The four authors are also co-authors of the Nature Astronomy paper. They state (my emphasis):

The detailed biosynthetic pathway for microbial phosphine production
is currently unknown. For detailed discussion of the biological
production in the environment, its biochemistry, and atmospheric
chemistry see three recent papers by Bains, Sousa-Silva and colleagues
[482,494,495].

These three papers are from the authors, one of which I followed up:

Bains,W.; Petkowski,J.J.; Sousa-Silva,C.; Seager,S. New environmental model for thermodynamic ecology of biological phosphine production. Sci. Total Environ. 2019, 658, 521–536.

The abstract to this includes (my emphasis):

In this paper we show through thermodynamic calculations that, in
specific environments, the combined action of phosphate reducing and
phosphite disproportionating bacteria can produce phosphine.
Phosphate-reducing bacteria can capture energy from the reduction of
phosphate to phosphite through coupling phosphate reduction to NADH
oxidation. Our hypothesis describes how the phosphate chemistry in an
environmental niche is coupled to phosphite generation in ground
water, which in turn is coupled to the phosphine production in water
and atmosphere, driven by a specific microbial ecology.

The paper itself is not of the ‘author-pays’ type, so you may need institutional access to read it. There is a graphical summary provided, however, which summarizes the hypothesis:

The paper consists of detailed thermodynamic arguments for the scheme suggested at the particular temperature, pH and anaerobic environment of marshes and swamps. Under these conditions, the authors postulate that the purpose of posphine production is to gain energy†. The analogy would be with the production of NADH as in anaerobic glycolysis to gain energy, but needing to be reoxidized to NAD+ to allow this to continue. The reduction of phosphate to do this would be analogous to the reduction of pyruvate to lactate or to ethanol. Like ethanol, phosphine would be a by-product of no value to the organism.
However the possible role envisaged for phosphine production in Venusian clouds is different. In the Supplementary Information for the Nature Astrobiology paper, there is the following:

Initial modelling based on terrestrial biochemistry suggests that biochemical reduction of phosphate to phosphine is thermodynamically feasible under Venus cloud conditions. Biological phosphine production on Venus is likely to be energy requiring. However, life can make substantial energy investment into compounds that provide important biological functionality. There are many potential useful biological functions including signaling, defense, or metal capture for which phosphine has useful properties, so endergonic biosynthesis cannot be ruled out.

The suggestion here is that phosphine is a useful product, synthesized at an energetic cost.
The only biochemical connection between the two would be that if, as appears likely, life on Earth can produce phosphine (by biochemical pathways that remain to be discovered), then these same biochemical processes would be candidates for phosphine production by life on Venus if the authors are correct in arguing that (at least known) non-biological candidates have been excluded. The question does not ask for opinions on the latter, nor would I presume to present those that I hold.

† The thermodynamic approach involves calculation of Gibbs Free Energy changes (ΔG) for reactions. Often on this site discussing standard biochemistry we (or at least I) talk in terms of standard free energies — ΔG˚ (or ΔG˚′ for normal cellular conditions). However the actual value of ΔG for a reaction is influenced by temperature and the concentration of reactants (which will include hydrogen ions), so that the ΔG calculated for terrestrial marshes and the like is likely to differ from that in Venusian clouds.


Examples of enzymes working in reverse? I have always been taught that enzymes can catalyze both the forward and reverse reaction, and will increase the reaction rate in both directions. I understand that the thermodynamics of the reaction are not altered by the enzyme, but I have yet to find a good answer / example for an enzyme that actually does this. (E.g. can a nuclease join DNA together if the products are in excess? Can a protease form a peptide bond?) I am having difficulty finding a resource online that actually justifies this claim without just saying "Yes enzymes work both ways."

Enzymes alter the rate of a reaction by lowering activation energy; they have no effect on the reaction equilibrium ($\ce{K_{eq}}$). Since $\ce{K_{eq}=\frac{k_f}{k_r}}$ and $\ce{K_{eq}}$ is constant, an increase in forward rate ($\ce{k_f}$) requires a corresponding increase in the reverse rate ($\ce{k_r}$). Intuitively it may help to think that the same effect an enzyme has on lowering the energy of the transition state in the forward direction should also be present in the reverse direction. Whether or not the reaction actually proceeds in reverse depends on the free energy difference between the reactants and products and their concentrations (among other things). See this answer for a great explanation.

Because their reactions are in equilibrium ($\Delta G\approx0,\ce{K_{eq}\approx1}$), many enzymes in the glycolytic pathway also catalyze the reverse reaction in gluconeogenesis.

[image source]


What prevents mRNAs that are localized to a specific part of the cell from being translated before they reach their destination? One of the methods of mRNA localization, for example, is random diffusion of mRNAs where the mRNA binding proteins are localized to a certain part of the cell. However, I was taught that the ribosome can translate mRNAs before they've even finished being exported from the nucleus. So what stops localized mRNAs from being translated all over the cell before they reach their designated location?

I was thinking maybe they're bound by hnRNPs that inhibit their translation, which dissociate when they're bound by localized mRNA binding proteins, but I could be wrong.

Or is it that they are translated all over the cell, but the concentration at their locale is just way higher in their locale?

The answer to your general question is 'it depends':

A lot of RNA localisation to the ER and mitochondria happens co-translationally (based on the protein targeting sequences), so these mRNA actually depend on translation to be localised. However, RNA localisation to mitochondria can also happen due to targeting sequences in the mRNA 3'UTR - in these cases translational repression would be possible, but it's unlikely and I don't think anyone ever checked it in this particular case. (see i.e. this review)
the translation of many mRNAs that are actively transported along the cytoskeleton is inhibited during transport, either by specific RNA binding proteins or larger RNP (ribo-nucleo-protein) complexes (see another review).

There are also bound to be some specific mRNA that have very specific regulation mechanisms and others that are exceptions.


Does a virus have a well defined shape? I assumed a virus to be something with a very specific geometry,
similar to a crystal, but more complex.

In an answer to
What is the size (diameter) of the SARS-CoV-2 virus? some SARS-CoV-2 virus particles are shown.

It looks like they do not have the same geometry.

They may be soft and influenced by external forces, but they could also be of different, but similar shape. Also, they could simply be defective in some way.

I assume a structure of the size of a virus is not rigid. Assuming no external forces, would multiple exemplars  of the same kind of virus have the same shape?
Can a virus have a different molecular arrangement, but be equivalent for biological purposes?

Some parts of viruses are consistently shaped, in particular anything that is made of multiple copies of a protein sticking together. There are methods to determine the structures of these regular components to high precision, like single particle analysis (eg. zika) and X-ray crystallography (bacteriophage HK97). Other parts of the virus are less consistent, either because they are flexible or because they are produced slightly differently each time. The nucleic acid core is often arranged semi-randomly, and the lipid envelope of many viruses can vary greatly, dependent on the process by which parts of the host cell's membrane is pinched off to create new viral particles. Here's an example of pretty extreme variability of influenza particles, based on what cell type they have infected. Virus particles with different shapes can be just as infectious, but if they are too large the number of new viruses produced by an infected cell may be too low.


If my sunglasses provide "100% UVA/UVB Protection" why can't look directly at the sun? Is it simply the amount of visible light entering the eye? I'm simply confused as to why experts say that sunglasses do not provide adequate protection when they are advertised as blocking 100% of the sun's harmful rays.

The damage to your eye does not only come from UV exposure, but also from infrared (IR) radiation. Your eye contains a lens that focuses the incoming rays to a narrow point. This point would get very hot if you looked directly into the sun. This is comparable to focussing the sun on a piece of paper with a magnifying glass, it would start to burn. Also, the rods and cones in your retina are only tolerant to a certain exposure of visible light.

Source: https://eclipse.gsfc.nasa.gov/SEhelp/safety2.html


How many almonds a day can cause toxicity for vitE? Vit E in high doses is dangerous for tissue. How many almonds a day taken regularly can cause this?

RDA
Males : 10mg/day
Females : 8mg/day
Pregnancy : 10mg/day
Lactation : 12mg/day

15 mg = 33IU for vit E

Requirement increase for higher intake of pufa

Pharmacological dose: 200-400 IU/day

You can eat bags and bags of almonds every day for years and not be in any risk of vitamin E toxicity. There are many, many cases of adults consuming 500+ mg of Vitamin E every day, for years on end, with no signs of harm.

In general though, the max daily recommended value of vitamin E consumption is 1000mg. One cup of almonds (100g, or ~100 kernels) contains a little under 30mg of vitamin E. That being said, you can consume over 30 cups of almonds in one day before reaching the daily recommended limit.

You would have to eat tens of hundreds of thousands of almonds for there to be any kind of health concern.. at which point, you would probably suffer from other conditions than vitamin E toxicity.

You (should) have nothing to worry about.

EDIT: Here are a couple sources...

This page has everything about recommended limits, research that has been done, tables with daily limit values, etc.
US Department of Health and Human Services - National Institutes of Health

  Research has not found any adverse effects from consuming vitamin E in food.

This page contains basic nutritional facts for almonds. A 95g serving is about 90 whole kernel almonds. Nuts, Almonds - Nutrition Facts

  Serving size 95 g ... Vitamin E (Alpha Tocopherol) 24.9 mg


Are some animals, like dogs and cats, color-blind and how do we know that? I have heard that some animals, including dogs, cats and donkeys, are color-blind. They cannot recognize any color. Is that true? And how can humans verify that animals are color-blind, or not? During evolution, has color-blindness not bothered them at all?

TL;DR: We have a good physiological understanding of how eyes work, so by examination of other species' eyes, we can tell a lot about what colours they are capable of seeing.

First, a little bit about the physics of colour

Light is made of photons, and each photon has a wavelength. The distribution of wavelengths coming from sunlight looks like this (wavelengths on the x axis):

Any perceived 'colour' is some sort of summary of the wavelengths of the photons which get into an animal's eyes.

Now, a little about colour perception

There are cells in the eyes which respond to being hit by photons: these are called rods and cones. Colour vision is principally achieved using the cone cells, which have a peak sensitivity at one particular wavelength, and are less sensitive at other wavelengths.

We (non-colourblind humans) have three different types of cone cell, sensitive to photons with wavelengths of 560, 530, or 420 nm, corresponding to the peak sensitivities of three different types of light-sensitive opsins which are present in cone cells. Other types of opsin exist in rod cells (Rhodopsin) and our circadian-rhythm entrainment (melanopsin), but the three different opsins in our cone cells are responsible for our colour vision. Because we have three different types of cone cell, we are referred to as 'cone trichromats'. The sensitivities of the three cone types overlap a bit, looking like this when plotted over the visible spectrum:

When cone trichromats perceive colour, what we're doing is taking the information on how active each of our different types of cone cell are, and using that to infer how many photons there are of each wavelength in the light that hits our eyes.

Of course, cone trichromats can't possibly summarise the whole diversity of wavelengths that are coming into their eyes using just three different measures of intensity - the line is way too complicated to summarise from three points. Also note that for humans, there is no cone cell that is sensitive above about 700 nm, or below about 400 nm. This means that we simply can't see differences in the infra-red or UV parts of the colour spectrum.

How does this all relate to colour-blindness in animals?

It is fairly simple to test the peak sensitivity of a cone cell: you take an eye from a freshly-dead animal, hook up an electrode to a cone cell, and then provide light of different wavelengths, and measure what wavelength causes the cell to 'fire' the most. If you repeat this with a large number of different cells, you can confidently determine how many different types of cone cell the animal has, and what wavelengths those cone cells are most sensitive to. This experiment (or similar ones) has been done for many different species, so we have a good background knowledge of what colours different species are capable of seeing.

Many species, including most non-primate mammals, have only two types of cone cell (i.e., they are cone di-chromats, as against non-colourblind humans, which are cone tri-chromats). This doesn't mean they see no colour, but it does limit the types of colour they are able to see. Many tools exist to simulate the visual ability of cone dichromats, for instance here, or here for browsers without flash support. These tools simulate human vision with different numbers of cone cell types. When comparing across species, it is important to remember that both the number of types of cone cell, and the peak sensitivity of each type, may be different, so the tools do not capture the full range of possible colour-perception abilities across species.

There are also cone tetrachromatic (four types of cone cell) and pentachromatic (five types) species. The record appears to be held by mantis shrimps, which have sixteen different types of cone cell. These species can in principle see a greater diversity of colours than cone trichromats.

Does colourblindness present an evolutionary problem?

Not necessarily. Compared to cone tetrachromatic species, humans are 'colourblind', and it seems to have very little impact on our day-to-day survival. Similarly, most colourblind humans (i.e., with one or more types of cone cell disabled compared to non-colourblind humans) get along perfectly fine - a special test is needed to detect colourblindness in humans. If trichromatic vision gives no particular survival advantage, there is no reason to think that it will be favoured by evolution.


Verifying Protein Folds I have recently begun using Folding@Home and I am curious how people are prevented from cheating the system. It seems to me that unless the final result is easily verifiable users could submit bogus folds in order to quickly gain credits. Is it in fact the case that the final results of calculating a protein fold are easily verifiable?

Besides duplication as verification there are numerous other computational methods to ensure that the result is valid. Proprietary software is used for folding at home so one can safely assume that they check hashes on processors and files regularly. If integrity is broken (by a crash, memory corruption or God forbid injection) the software client side and server side trashes the result. One can imagine that faulty hardware or other problems can result in a ban from the servers.


Why do organisms excrete nitrogenous wastes? Organisms excrete nitrogenous wastes in the form of urea, uric acid or ammonia. But isn’t that a bit of a waste? There is a shortage of biologically available nitrogen in the ecosystem, and plants convert nitrogen in ammonia and nitrates into amino acids. Why do organisms then deaminate these amino acids and then excrete them?

It seems to me that it would make much more sense to store the nitrogen for further use. I understand that ammonia is toxic, but surely it could be stored in some specialized structure.

Some amino acids are essential, that is, they cannot be synthesized.  For all the others, however, you need building blocks.  Nitrogen, and specifically ammonia, is required for non-essential amino acid synthesis, the transfer of which is accomplished through a process called transamination.  Amino acids are also broken down for energy as a metabolic process, producing glutamate (in addition to energy-containing molecules such as pyruvate).  The body has thus produced some amino acids and metabolized others for energy,  but glutamate must be deaminated to remove the nitrogen, which by this point is now in excess.

To evolve a specialized storage unit for highly toxic substances could be useful, I suppose, but it would be unlikely and would pose a huge risk compared to just getting rid of 'em.  I'd rather urinate a few times a day than save a lot of toxic material for later and run the risk of something malfunctioning and killing me; besides, eventually that storage unit would get full.  You could ask the same question for any substance we might eventually want.