Why a continuous supply of energy is needed to support a weight? What motivates this question is the apparent discrepancy between the concept of Work in physics and in physiology.
Work in physics is defined as the dot product of the force applied to move a certain object by its displacement:
$W = \vec{F} \cdot \vec{d}$
$\text{ Work  =  (Force) $\cdot$ (Displacement)}$
Where $\vec{F}$ is the force vector, and $\vec{d}$ is the displacement vector.
Now if there is some weight lying on a table, it takes no Work at all to maintain its present configuration, since both $\vec{F}$ and $\vec{d}=0$, As a result $W=0$. In other words, this weight-table system does not need to be provided with energy at all, for the table to be able to support the weight, because it takes no energy to support it.
What about an identical case but with a human hand supporting a weight(at a constant height) at this time? Although according to the above reasoning one should expect that it does not need any energy to support the weight, this is not what we observe in everyday life, because when I hold the weight, it takes a tremendous amount of effort to support and maintain its position.
When I looked up the reason behind this, I found out that it has to do with the fact that the muscles of the arm are skeletal muscles not a smooth one.
If the arm were made out of smooth muscles, then it would take no effort or energy at all to support any weight at a fixed height.On the other hand, the muscle fibers that contract to support the weight in Skeletal muscles has to be continuously provided with energy to be able to support it, and hence although no mechanical work is applied on the weight so $W=0$, nevertheless energy is wasted in the form of heat in this process, and hence we get tired after holding an object for some time.
So what is the mechanism by which Skeletal muscles support certain weight? Why it needs continuous supply of energy while holding an object? How is this energy supplied( my guess is:some component of a cell breaking down molecules so as to transfer chemical energy to mechanical contraction of muscle fibers)?And how it differs from smooth muscles?

For skeletal muscles, you'll find a discussion in the Physics SE: https://physics.stackexchange.com/questions/1984/why-does-holding-something-up-cost-energy-while-no-work-is-being-done

To make things short: while holding a position, muscles need to maintain a given length. However, internally, the muscle looks like a collapsible array of filaments, with myosin heads acting as crossbridges between them. Even when the muscle is not contracting, myosin heads unbind and rebind at some rate and would let the muscle relax -- unless you input more energy to compensate this with a further contraction.

For smooth muscle, according to this article, the rate of unbinding can be very slow:

  Once the contraction has occurred, the cross bridge attachments need
  to be released in order that the muscle can relax. Although less is
  known about this phenomenon, it appears to be related to
  dephosphorylation of MLC20. In some situations, the dephosphory- lated
  MLC20 is very slow to allow detachment of the actin from the myosin
  cross bridge, resulting in a prolonged contraction. This has been
  referred to as a ‘latch-bridge’ (Hai and Murphy, 1988). This
  phenomenon may be of great value especially for tonically active SM
  beds as it would allow them to maintain basal tone through holding in
  an isometric state without a great energy cost.

So as the muscle is not relaxing, no input of energy is needed to adjust its length to the desired one. I assume a disadvantage of that is that the reaction time of the muscle is slower.


White resin or powder on conifer needles I often notice that certain conifers often have a whitish powder on what seems to be their youngest needles, giving them a blue green tint. Does anyone know what this is? Is it something excreted by the trees themselves, is it a yeast or some other endophytic microorganism? Very curious and unfortunately I don't have a microscope.

I believe this is actually crystallized sap which formed on and around the bud as the bud opened up and new leafs emerged.

Note that some coniferous trees have a powdery coating as part of the leaf itself, continuing on throughout the life of the leaf. Blue spruce is a good example of this, as its dark green needles appear blue/gray due to a waxy coating the needles. This wax can be easily scraped off the leaf.


How does sunlight affect the longevity of SARS-CoV-2 on surface? UV radiation is known to degrade most viruses rather quickly.  How does the UV radiation from sunlight affect the longevity of SARS-CoV-2 on surfaces.

Of particular interest to me is the virus' lifespan on gas pump handles, which are typically in covered but open spaces.

I have no data on SARS-CoV-2 specifically, but for SARS-CoV UV radiation is an effective method of eliminating viral infectivity:

Irradiation of UV for 60 min on the virus in culture medium resulted in the destruction of viral infectivity at an undetectable level.
CONCLUSION: The survival ability of SARS coronavirus in human specimens and in environments seems to be relatively strong. Heating and UV irradiation can efficiently eliminate the viral infectivity.

Stability of SARS coronavirus in human specimens and environment and its sensitivity to heating and UV irradiation., Biomedical and Environmental Sciences (2003)


Are ape communities more "anarchist" or "communist" in structure? I am using these terms because we can imagine them quite good, I guess ;)

By "anarchist" I mean that the ape wants to live without the rule of others apes(same biological race or other) and he pursue his own goals (replication, getting food etc.)

By "communist" I mean working together in groups because of the "higher"purpose (better chance to protect themselves, getting food easier, other benefits)

I am particlarly interested in apes, excluding us, of course.

Among the great apes, chimpanzees and gorillas live in very hierarchical, male-dominated clans that are often in violent conflict with other clans. Bonobos, on the other hand, lead very peaceful lives, and are female-dominated, using sexual contact as a manner of communication to reduce tension within and between groups. Orangutans are largely solitary animals, with heavy parental investment (7 years, longest among non-human primates), wherein the mother lives separately with her child during the early years of development. Among the lesser apes, gibbons and siamangs are also highly territorial and pair-bonded, though notably, polyandrous siamang groups have been shown to display higher degrees of cooperation.

Though Anarchism varies greatly between different definitions, the most popular form of contemporary Anarchism values non-hierarchical organization, centered around mutual aid, rather than the kind of isolated individualism that you seem to associate with the term. By this definition, bonobos would be more "Anarchist" than chimpanzees. By your definition, orangutans might be the most "Anarchist."

Your definition of "Communism" is closer to the contemporary definition of Anarchism above, due mainly to the historical trajectory of Communism, which in practice, did not work out so well, leaving contemporary utopian thinkers largely in the Anarchist camp. By your definition of "Communism," bonobos may be the most "Communist"; however, if you mean the state-based gulag Communism of popular culture (ie portrayals of the Soviet Union), then you might say that chimps were more Communist. This is because individual chimps sacrifice individual goal attainment for group ends under the coercion of the alpha male chimp. Of course, some people may call that Fascism.

You may want to take a look at primatologist Franz De Waal's research on bonobos vs. chimpanzees. As a pacifist, he has a bit of an agenda, in terms of trying to prove that female-dominated bonobo "societies" are inherently more cooperative and less hierarchical. Another primatologist that agrees with this view is Harvard primatologist Richard Wrangham, who looks at hierarchical organization and violent behaviors in chimpanzees.

Robert Sapolsky's research on baboons may also be of interest to you. He found a clan of baboons, in which all the alpha males had died from tuberculosis due to exposure to an infected meat found in a neighboring human village. He noted, then, that the remaining baboons lived much more peaceably and cooperatively than other observed clans, and furthermore, that this clan retained its "culture" and passed on its more cooperative ways of behaving to new members in the clan, therefore demonstrating that perhaps baboons (and other primates) are capable of having and passing on "culture." - Perhaps a more "Anarchist" culture than nature normally prescribes.

However, as a caveat, I must say: it is tenuous to make direct associations between ape behavior and human societies. Human culture, social intelligence, and symbolic reasoning facilitate human political systems. Though Sapolsky's work suggests primates may also be capable of some form of "culture," biological descriptions of ape social organization is insufficient to explain human behavior.


Goats are so fearless but sheep are not. Is there any genetic difference responsible? As you see in the picture goats (not only wild goats) are so fearless, but I never saw any sheep do this. What is the source of this difference in behavior?

1. Sheep are fearless

2. English common names are misleading when it comes to the genetic differences between goats and sheep

You posted a picture of Mountain Goats (Oreamnos americanus), which are a different genus than Domestic Goats (Capra aegagrus). Both Capra and Oreamnos are members of the Subfamily Caprinae, as are Domestic Sheep (Ovis aries).

Within Caprinae, Capra and Ovis are actually more related to each other than either one is to Oreamnos, despite the confusing way that we parcel out English common names. Oreamnos is, in fact, more closely related to the Musk Ox! (Here's the Tree of Life page that shows the phylogeny of Caprinae).

The Domestic Sheep genus Ovis also includes mountain species such as the Bighorn Sheep Ovis canadensis, which is plenty fearless. See the Bighorn Sheep above, and in this incredible photo. For what it's worth, the Domestic Goat genus Capra also includes cool mountain species, such as the Ibex.

Edit: the differences in behaviour between the domestic goat and sheep would be a combination of the initial differences between wild Ovis and Capra and the coevolutionary process of domestication; where humans shape niches to fit animals and animals to fit niches. It's possible that there has been more neotenization in the domestication of sheep, in which individuals who show immature characteristics are successfully selected for. See also this other question on apple and pear domestication.

(Bighorn Sheep photo by TwelveX, used under CC BY-NC-SA license.)


How do fatty acid and polyketide synthases handle the varying size of their substrates? Polyketide synthesis involves six modules, each containing certain common constituent enzyme activities (KS, AT, KR) that are involved in extending the chain (see e.g. Dutta et al.(2014) ). The growing polyketide, attached to acyl carrier protein, is passed on from one module to the next.

An analagous situation is seen in the single Fatty Acid Synthase complex. How can the same enzymes in later modules recognize what is a structurally different intermediate? Surely this contradicts the idea of substrate specificity of enzymes.

Although the substrate is different at each stage of chain extension,
  the part involved in the reactions — and recognized by the enzyme — is
  the same. This is a common feature of polymerization reactions,
  whether the catalysis is by a single module (ribosomes, DNA
  polymerase) or multiple modules (polyketide and fatty acid synthesis).

This is illustrated by the modification made below to a part of Figure 1 of the paper cited in the question. An overlay in yellow has been made to indicate the common structural features of the polyketides of different length.

Of course, the rest of the chain may well interact with the enzymes, but as this is not at their active sites it can be in a less specific manner, perhaps in a ‘groove’ containing appropriate interating chemical groups.

The question of substrate specificity is not the point of interest in the paper on polyketide synthase where the focus is on the way the elongating substrate is passed from enzyme to enzyme and module to module (the resolution is also too low). It has, in any case, been addressed in previous work on mammalian fatty acyid synthase, where exactly the same single (dimeric) multidomain complex acts on each intermediate until the chain length is 16-18 C atoms. However the question of chain length is taken for granted and the discussion is about discrimination between chemically different intermediates. Thus in a 2008 paper by Maier et al. a substrate tunnel in the ketoacyl synthase (KS) module of the fatty acid synthase (mFAS) is compared with that in polyketide synthase (PKS):

  “Despite the pronounced structural similarity between the KS domains of mFAS and PKS, the selectivity of FAS for saturated acyl chains can be explained by a considerable constriction at the base of the active site phosphopantetheine binding pocket leading into the large acyl chain substrate binding tunnel, which connects both active sites of the KS dimer (Fig. 4, A and B). A number of residues lining this narrow tunnel are highly conserved in mFAS but are substituted with smaller residues in all DEBS (6-deoxyerythronolide B synthase) PKS modules (Fig. 4B), resulting in a wider, more permissive tunnel in the KS of DEBS.”

It is important to think of substrate specificity in molecular terms — e.g. what part of the substrate binds to the enzyme and how specific has the binding to be. In this case the substrate is attached to the long phosphopantetheine chain of acyl carrier protein, so that recognition of that and the part of the fatty acid or polyketide attached to the sulphur may be enough to discriminate against ‘free’ extraneous molecules. And a tunnel is permissive as a binding site: if the chemistry and radius are right, there is no need for the whole of the tunnel to be occupied.

Tunnels of various types are found in other enzymes or organelles involved in elongating molecular ‘chains’, e.g. polypeptides and nucleic acids. The tunnel on the ribosome and that through which RNA or DNA passes has to accomodate chemical disparate molecules (four different bases, 20 different amino acids).


Hardy Weinberg equilibrium Hardy Weinberg would predict that the frequency of normal females, to carrier females,
  to affected females for colorblindness is equal to p$^2$ + 2pq + q$^2$=1. You
  were told that q=freq of the recessive allele. If p+q =1 (frequency of the dominant allele +
  frequency of the recessive allele=1 or 100%) and q=.08, what is the frequency of the
  normal allele in the population? What is the frequency of carrier females in the
  population (ie heterozygous females)?

I get that the frequency of the normal allele is p = 1 - .08 so 0.92. However the frequency of carrier females is giving me an unrealistic number. Using p$^2$ + 2pq + q$^2$ =1, the value for pq comes out to be a negative value. Is it safe to just multiply p and q since that is what we're essentially solving for using the full HW equation? This would make the value (.08*.92) = 0.0736. Would that be the way to approach the problem even though it asks for females only?

Carrier females= 2pq= 2 x .08 x 0.92

Because carriers say with genotype  Aa (A=dominant, a=recessive)  can arise due to two types of inheritances;one when A is from father and a is from mother and the other when it is just opposite.


Is this an insect? Which one? I found this animal, which I suspect it's an insect, on the floor of a kitchen in Spain some days ago. It's about 8-10 mm long. I don't think I've ever seen it before. What is it?

It is a silverfish. It is a 'basic lineage' in the insect class. You'll find it here on OneZoom.org.

Silverfish are considered household pests although I don't think they spread disease nor cause much damage (thanks to @WilliamBligh for his comment). They typically live in the canalization (bathroom, kitchen) or anywhere that is wet enough. In a building, they may be hard to get rid of as they can easily move from one apartment to another. You have to keep your place very clean and eventually use toxins such as Permethrin or Deltamethrin.


Difference between rate of elimination and clearance? I honesty don't get the difference. I need a simple explanation so that I can grasp it.
Rate of elimination is

Clearance is a measure of the volume of plasma from which something is removed, per unit time. For instance, it could be 2 mL/min, meaning that every minute, a two-milliliter of drug plasma is cleared. In other words, it is the rate of drug elimination divided by the plasma concentration.

Remember that the elimination rate is in units of inverse time, so dividing it by inverse volume gets you volume over time, which is the standard dimensionality of clearance.


What is the reproductive success of a biting mosquito? Female mosquito can lay ~50-100 eggs in each batch. It takes some time between the hatch and until the time the female mosquito bits. During this time many of them will die.

What is the average percentage of the eggs that mature (in other words, if a female mosquito lays one hundred eggs, how many of them will become grown females that bite)?

The amount (percentage) of eggs to mature varies greatly and depends on many factors and off course varies by season.

The correct (but not really satisfying) answer is that from every 100 eggs, between 0 and 100 eggs will mature. On average, this number is greater than 1 (otherwise the species would go extinct), and much smaller than 100 (otherwise the world would drown in mosquitoes). Because the question doesn't include the complete lifecycle, it is not exactly 1, but greater than 1.

Some explanation
Mosquitoes lay eggs in water, and the larvae are easy prey for predatory invertebrates (larvae of dragonflies, beetles etc.) and fish. Many mosquito species choose small, isolated waters (like small pools and plant-pots) where there is likely to be little predation. This however carries a risk: these waters often dry out (reproductive succes 0%), offer little resources (reproductive succes low) and offer no shelter against an unforseen predator (reproductive succes low). If they choose wisely however, reproductive succes can be very high. Because of this large variation, an average number is really not so informative.


Why are transmembrane proteins difficult to crystallise? I know that in vivo there are a lot fewer transmembranous proteins in general, and that they are produced at a lower rate than their free counterparts. This is mainly because transmembrane proteins are only required in a 2D space on the membrane rather than a 3D cytoplasmic or extracellular space. This (again, very broadly speaking) means that the probability they will interact with their target is higher.

I also know that this is one of the reasons that producing crystals for X-ray crystallography is notoriously difficult for transmembrane proteins. What are the other reasons that make transmembrane proteins typically tough crystallisation candidates?

What specific part of the crystallisation process yields such poor success rates of transmembrane protein structure elucidation?

There are several factors that make obtaining crystal structures from membrane proteins more difficult.  In brief, nearly every stage of obtaining the structure via crystallography is more difficult.

First: protein expression.  Large amounts of pure, well-folded protein are required and this is much more difficult to achieve than it is with a soluble protein. Since membrane proteins are bound within a membrane, the mechanisms to translate the peptide into the membrane and to fold the protein in the membrane are different.  They may involved folding factors which are only available in a particular compartment of the cell (making bacteria impossible as a system of expression).  In high amounts in the cell, their hydrophobicity might tend to result in clumps of unfolded protein instead of gobs of membrane-associated protein.

Next: Purifying the protein is more difficult.  The expressing cells are usually broken open in the presence of detergent to get the proteins to float around as individual proteins in detergent micelles.   The wrong detergents might break up the membrane protein and it may lose its fold - the concentration of detergent must be carefully managed and kept at optimal levels or the micelles might break up and the protein will be ruined.

Crystallizing the protein is quite a bit more difficult too.  Membrane proteins in detergent micelles which may or may not be charged themselves look like oily blobs with hopefully a domain or two of folded proteins sticking out of them.  Compared to a soluble protein with a nice ordered surface in every direction instead of a detergent micelle which might undergo a phase change at high concentration or by the addition of a salt or change in pH, membrane proteins take a task that might take thousands of trials and adds new dimensions to worry about.

The proteins are 2D-like, but the crystals still have to be 3D for crystallography to work usually.  Protein crystals are small, but those derived from membrane proteins - which tend to organize into planes like the membranes they inhabit - are often thin, which can make them too delicate and small to get a good set of data even from synchrotron beams.  As a result, the crystals are commonly too small or thin to use at first, requiring extensive optimization after the first crystal are found.

In a few cases some membrane proteins have been solved with 2D crystals using electron microscopy on crystalline arrays of porins and rhodopsins in membranes. That was a ton of work but they were the first membrane protein structures by years and years.

Not to make all this sound impossible - once you have crystals, they can usually be improved; there are good starting points to crystallization and purification with detergents.  It's just that a process which can already take quite a bit of time (years) and can sometimes end in frustration takes even longer and is less certain with a membrane protein.


Why do F- bacteria still exist? When an F+ bacteria conjugates with an F-, it makes the other bactaria F+ too. So on the long run, all bactaria should be F+.

Is there any mechanism that converts F- to F+? Could it be degeneration of F plasmid?

So an easy way to convert a cell from F+ to F- is to divide it without correctly replicating the plasmid and transferring it to a daughter cell, leaving you with one F+ and one F-. The cells that are F- now have a selective pressure advantage over the F+ cells, as they now don't require the energy to produce a plasmid when they divide. If that advantage is enough to overcome the frequency of conjugation, you'll end up having a population of F- cells.


Do different species of bacteria have distinct absorption bands? Do bacteria of different species absorb different wavelengths of light? How different?

Most of my searching has lead to topics about Optical Dispertion which seems to be species independent as opposed to single species.

Yes they do, as demonstrated by the fact that bacteria have different colors ! Moreover, some bacteria are photosynthetic and others aren't; the photosynthetic bacteria have a very specific mechanism for absorbing light that the others don't so it stands to reason they won't absorb the same wavelengths.

This page talks about it very nicely, with a list of different colors and bacteria that have them:
http://www.biotecharticles.com/Applications-Article/Colorful-Bacteria-612.html

Money quote :

  Bacteria are pigmented or colored. Pigmented bacteria are also known as chromobacteria. Bacterial pigments are water soluble or insoluble; water soluble pigments are diffused in the growth medium. Chemically, bacterial pigments are pyrrole, phenazine, carotenoid, xanthophylls and quinine or quinone derivatives. The pigment molecules are synthesized in cell wall or periplasmic space. We can visualize pigmentation in bacteria in specific growth medium or my staining bacterial cells with a dye to observe under microscope. It has been proved that only aerobic and facultatively aerobic bacteria are pigmented because, molecular oxygen is essential for pigmentation. Therefore, anaerobic bacteria are nonpigmented. Pigment synthesis is also dependent on light, pH, temperature and media constituents like indicator dyes. They display all the colors from rainbow including light or dark tinges and unual colors like black, white, brown, golden, silver and fluorescent green, yellow or blue.

And the list:

  Purple: Spirillum rubrum
  Violet: Chromobacterium violacein
  Indigo: Janthinobacterium lividum
  Blue: Streptomyces coelicolor
  Green: Chlorobium tepium
  Yellow: Xanthomonas campestris
  Orange: Sarcina aurentiaca
  Red: Serratia marcenscens
  Brown: Rhizobium etli
  Black: Prevotela melaninogenica
  Golden: Staphylococcus aureus
  Silver: Actinomyces sp.
  White: Staphylococcus epidermidis
  Cream: Proteus vulgaris
  Pink: Micrococcus roseus
  Maroon: Rugamonas rubra
  Fluorescent blue/green: Pseudomonas aeruginosa
  Fluorescent yellow: Pseudomonas fluorescens

It appears some purposes of producing pigments, aside from photosynthesis, are to absorb UV light (i.e. absorbing a specific wavelength is the entire point) or mopping up free radicals.

An additional note, from the Wikipedia page for Rhodospirillum rubrum, the first bacterium in that list (which Wikipedia describes as "pink" but close enough):

  The photosynthesis of R. rubrum differs from that of plants as it possesses not chlorophyll a, but bacteriochlorophylls. While bacteriochlorophyll an absorbs light having a maximum wavelength of 800 to 925 nm, chlorophyll absorbs light having a maximum wavelength of 660 to 680 nm.

https://en.wikipedia.org/wiki/Rhodospirillum_rubrum

And while that paragraph describes "chlorophyll a" as being a feature of plants, other bacteria do use it such as Chlorobium tepidum, so there you can see some wavelengths that are absorbed by one and not the other.


Does our brain contain an innate function about closing only one eye? I wasn't sure where to post this, but biology seemed fitting for me. Sorry if I'm wrong.

I was wondering why, when we close both our eyes and look at light, it is clear we can see the light even though our eyes are closed. We can identify where the light is too.

However, when you look at the light with only one eye closed, suddenly you cannot perceive this anymore and you can only focus on the open eye's vision. It's like our brain is ignoring the closed eye's vision somehow. What is triggering this "ignore vision"? Is it the closing of the eye?

I found this intriguing and wondered how this works and/or if there is any research about it.

I'm only a 17 years old student but i guess this is the answer(its just what i guess, haven't seen it in any books or research):

This is a picture from the book Life.
When both eyes are working they send signals to brain.
signals from things on the left side are sent to right side of brain and signals from things on the right side are sent to left side of brain(coming from both eyes).
as you can see both eyes participate in sending signals to right and left hemisphere.

On the right side of picture you can see visual cortex of right hemisphere , it has signals coming from both left and right and makes the thing we see.

While seeing through only one eye (or when you cut optic nerve from one eye) there is still signals coming to visual cortex from the other eye and that makes image of what you see.(when you close one eye there is still little signal from it if you are facing a bright light source, but signal from the other eye has more effect as its more powerful( try it by closing one of your eyes and put a torch in front of only the closed eye, if the torch is bright enough you can see bright thing there))

when you close both eyes the signals coming from both eyes are almost the same and if you face a bright thing, you almost see it.

i just guess that's the mechanism :)


Non-coding DNA as a protection to deleterious mutations We know that most part of our genome (at least 75 percent) is non-coding DNA. Can it be a way to protect the organism from mutations in important genes, such as the ones which control cellular cycle, as a mutations is much more likely to occur on these parts of the genome?

I've never been told if it could have such a function, and I thought about recently and wasn't able to find a clear answer.

So thanks in advance

You seem to be under the impression that there are a set number mutations per cell, which is not true.  The number of mutations is roughly proportional to the number of bases  — this is because mutations typically happen as a result of errors during DNA replication .1  Consequently, more DNA will not protect the coding portions of the genome from mutation.

The reason why mutations appear to be suppressed in coding regions is due to selection.2

References:
1: Lodish, H., Berk, A., Zipursky, S. L., Matsudaira, P., Baltimore, D., & Darnell, J. (2000). Molecular cell biology 4th edition. National Center for Biotechnology Information, Bookshelf.

2: Griffiths, A.J.F., Gelbart, W.M., Miller, J.H. and Lewontin, R.C. (1990) The Molecular Basis of Mutation. In: Modern Genetic Analysis. W.H. Freeman and Company, New York.


How do non-dimorphic birds distinguish sex of possible partners/rivals? Some birds, such as my pet Pionus chalcopterus, are not sexually dimorphic.  People can't tell them apart, and even trained avian vets are not 100% certain with an inspection probing the vent.

I understand that when not "in season" there is no physical difference as internal sex organs are atrophied to save weight.

But how do they tell the difference?

Do they have dimorphic markings that bird eyes (but not humans eyes) can see?

As very well explained also in Wikipedia https://en.wikipedia.org/wiki/Sexual_selection_in_birds , visual signaling is only one of the way birds uses to pick a partner, olfactory and acoustic signals also play a major role.


Why spin live fruit flies in centrifuge? I was reading this article about the evolution of monarch butterflies’ resistance to cardiac glycosides: These Butterflies Evolved to Eat Poison. How Could That Have Happened?
And this passage made me curious:

The researchers put the mutant flies in a centrifuge and spun them for ten seconds. Afterward, the flies were overwhelmed by seizures for several minutes.
Ordinary flies, by contrast, immediately walked away from the laboratory carnival ride. Flies with the other two resistance mutations were also unharmed by the procedure.

Given that normal fruit flies are usually unharmed by the centrifuge, what made the researchers decide to spin the flies? I’m not a biologist, I’m a software engineer. So I’m just guessing that it might be a standard lab procedure when studying fruit flies. Assuming the researchers didn’t know the flies with mutation 122 alone would experience seizures, what do researchers usually expect to gain from spinning live flies in a centrifuge?

Correction of Poster’s Source

The article cited mistakenly refers to centrifugation, however the actual procedure used in the work — Karageorgi et al. Nature, 2 Oct 2019 — is vortexing, as illustrated in Fig. 3 of the paper below.

What is meant by standard lab procedure?

  There is no such thing as standard lab procedure. There are standard
  lab procedures for performing certain kinds of experiments or processes.

In studying the effect of mutations on the behaviour of live fruit flies one devises laboratory procedures that are, if at all possible, cheap and easy to perform on many animals. All laboratories have vortex mixers of the type illustrated, as these are used to speed up dissolution of solutes and to disperse (resuspend) solids which have been precipitated by centrifugation — perhaps the source of confusion as the flies would likely have been put in centrifuge tubes as these would be appropriate (although the flies were not subjected to centrifugation).

Why vortex flies?

The vortexing is what is apparently called a ‘Bang’ assay — a means of testing flies for neurological seizures. The authors state:

  To investigate this, we phenotyped monarch lineage knock-in flies for neurological seizures upon shaking (bang sensitivity), a common phenotype in hypomorphic Na+/K+-ATPase mutants29,30

Without consulting references 29 and 30, it seems clear that the authors were expecting cardiac glycosides to produce neurological seizures, and used a simple technique that had been used previously by others to assay this.

So, yes, if you are interested in these aspects of fly physiology vortexing may be a standard laboratory technique, but, no, other fly labs (e.g. those studying the gut) don’t start the morning by saying:

  “Lets take the new mutant for a spin”.


What is the convention for indicating genomic primer sites? What is the most common notation for indicating genomic binding sites of primers relative to an ORF?

For instance, if I want to indicate a primer like so:

...tccgccGCCCGTCCACACCCGCCGCCagctcaccATGGATGATGATATCGCCGCGCTCGT...
         [ Primer           ]        [ Hs ACTB coding sequence   ]

Should the location of this primer be indicated as -8 or -28 (from ACTB start codon) or something else?

There is no such convention. People, mostly name their primers arbitrarily (or just FP and RP) and mention in the text about their binding sites.

In general, in the context of specific genes, the positions are described with respect to the transcription start site (TSS).


Are all animal species prone to cannibalism induced prion infection? Humans have the tendency to get certain prion diseases when eating human flesh. It's known animals can get prion diseases as well.

Does cannibalism among other animal species also make them more susceptible to get a prion disease, and are there distinctions between mammals doing so and other orders like reptiles, birds, fish etc.?

An individual (animal or human) acquires a prion disease when they consume meat that contains prions (proteins that are mishapen enough to drastically change their functionality), which subsequently causes proteins within the individual to misfold into the same shape as the prion, resulting in a whole slew of problems.

As of right now, there is little knowledge of where prions come from/how they're formed. Also, there is little knowledge of how inter-species infections/transmissions occur. Researchers are currently investigating various combinations of inter-species transmissions, such as humans eating infected horse meat, or cats eating infected chicken meat, but still know only very little about this phenomenon.

To say which species have higher rates of prion disease when looking at a cannibalist communities within that species, I don't think we're anywhere near close to making those conclusions, and the same goes for inter-species transmissions.

All the best.


Are there any examples of predators that ambush scavengers? I'm specifically asking about animals that use a hunting strategy revolving around hanging around cadavers to attack animals attracted to the cadaver, or even leaving part of their catches out to lure scavengers.

Saltwater crocodiles in Australia are reputed to do this; storing meat under water and later eating the fish and crustaceans that are attracted.
Having trouble finding a good source for this.
Article from national news service below.
https://www.abc.net.au/science/articles/2004/01/15/2045125.htm
Feel free to add references if you can find them.


Adam's Apple and Voice box Why is Adam's Apple more prominent in males? Is it due to bigger voice box pushing the cartilage more, or is the cartilage indeed bigger than that in females? I am assuming bigger voice box as males have a "deeper" sound. Is it correct to do so?

Yes, you nailed it!

Adam's apple (aka.  laryngeal prominence) exist in both men and women. It is a piece of bony cartilage called thyroid cartilage that wraps around the larynx (aka. voice box).

The Adam's apple is more prominent in males because males have have a bigger larynx (giving males a deeper voice). In males, the prominent Adam's apple typically appears during adolescence, when the larynx increases in size and the voice becomes deeper.


Furry Bug that swarms only certain plant What is this strange bug?

It swarms only on one certain plant with trumpet-shaped red flowers (in the picture the flowers are all shriveled and the leaves are in the foreground) and totally coats it until the bush dries up. It spreads very rapidly but only to this particular plant - will not touch any other. The bugs don't noticeably move, giving the impression that the whole bush has developed white fur.

Picture taken in Israel:

EDIT:

Here's a closeup of a single specimen (taken from one of the leaves in the foreground):

And it seems the plant is a hibiscus:
http://homeguides.sfgate.com/hibiscus-leaf-87355.html

As indicated in @KarlKjer 's comment, this insect is a Pseudococcidae, or commonly known as Mealybugs. The exact species is difficult to find due to picture quality.

Mealybugs are insects in the family Pseudococcidae, unarmored scale insects found in moist, warm climates. Many species are considered pests as they feed on plant juices of greenhouse plants, house plants and subtropical trees and also act as a vector for several plant diseases.
Mealybugs occur in all parts of the world. Most occur naturally only in warmer parts, and get introduced into greenhouses and other buildings in cooler countries. It is unlikely that any live in the Arctic or Antarctic, except perhaps in buildings.

Considering that Mealybugs are found basically anywhere on Earth, it's not a surprise to have found them in Israel.


When do the first neurons appear in humans? According to this

Neural Plate

The neural plate appears in day 18 in humans (very specific).

and according to this

Neural Plate (wiki)

  The progenitor cells that make up the precursors to neural tissues in
  the neural plate are called neuroepithelial cells.

And according to this

Neuroepithelial cells

  Neuroepithelial cells are the stem cells of the central nervous
  system, known as neural stem cells, and generate the intermediate
  progenitor cells known as radial glial cells, that differentiate into
  neurons and glia in the process of neurogenesis

So, if it's known when the cells which are precursors of neurons appear, I suppose it should be known when the first neurons appear, but I can't find information about it.

When do the first neurons appear in humans?

Apparently, olfactory axons and GnRH producing neurons are among the first neurons that migrate from neural crest at around 39th day of gestation in humans (Cassoni et al., 2016).

  In rodents, early GnRH neurons migrate together with a heterogeneous
  coalescence of placode-derived and neural crest-derived migratory
  cells (Forni et al., 2011) and olfactory axons, collectively called
  the ‘migratory mass’ (MM) (Miller et al., 2010; Valverde et al.,
  1992). This cell migration precedes the targeting of olfactory sensory
  axons to the developing olfactory bulb (OB). The existence of a
  similar MM in the human embryo has not yet been described. We thus
  immunolabeled consecutive sagittal sections of a CS 16 embryo† for GnRH
  and doublecortin (DCX) (Fig. 1D,E,G), a marker of immature migratory
  neurons (Gleeson et al., 1999). We identified a very small number (50
  in total) of immature GnRH-expressing cells in the nasal mesenchyme,
  in the medial portion of the olfactory placode (Fig. 1C-E), adjacent
  to the basal lamina of the VNO, showing that the acquisition of cell
  identity occurs outside the VNO between GW 5 and 6. At this stage, we
  observed a mixed mass of immature GnRH neurons expressing DCX (Fig.
  1F,G) or βIII-tubulin (Fig. 1H-J), migrating across the nasal
  mesenchyme towards the telencephalon. As in rodents (Miller et al.,
  2010), GnRH neurons in humans only represented a small proportion of
  the MM (Fig. 1G). Furthermore, these pioneer neurons of the MM
  expressed the delta/notch-like EGF repeat containing (DNER) (Fig.
  1H-J), a transmembrane protein specifically localized in the dendrites
  and cell bodies of postmitotic neurons.

  †Carnegie stage (CS) 16 = ∼39th day of gestation


How could this fossil's soft tissue be preserved so well? I found this article for non biologists like myself. It describes, how astounding fossils were found in China. They belong to a crustacean like animal that lived more than 500 Ma ago. The exciting thing about them is, that the nervous system -soft tissue - is fossilised in its finest detail. The article says:

  “Using fluorescence microscopy, we confirmed that the fibres were in fact individual nerves, fossilised as carbon films, offering an unprecedented level of detail. These fossils greatly improve our understanding of how the nervous system."

My question is: how can these soft tissues be so well preserved?

I managed to find the scientific publication   and attempted to identify the answer myself, but it seems to me, the question is not touched upon. Perhaps, being a layman, I overlooked it, or it is obvious to biologists?

You're right that the authors don't comment on how they think the fossilization occurred. Since that process isn't the point of their article, my guess is that any discussion of it would have detracted from their research focus.

There are some ways that soft tissue fossilization can occur, but to specifically answer your question as it relates to this case, you'd have to know more about the geological conditions in which the fossils were found, which I don't see in the article. This article provides a nice review of soft-tissue preservation processes.

The main points to consider in soft-tissue fossilization, according to the linked article, are pressure, time, charge and chemistry.

Pressure: How much pressure was the fossil under? The higher the pressure, the less oxygen and fewer organisms can access it and degrade biological tissue.

Time: How quickly did the fossil become inaccessible to degrading organisms? The faster this occurs, the less likely that any soft tissue will rot away.

Charge: Does the sediment in which the fossil found carry a charge? Electrical charge acts both as an selective barrier to some organisms and chemical compounds that can hurry biological decay and provides a means for reaction with biochemical compounds, which brings us to the last point:

Chemistry: Can components of the biological soft tissue react with their surrounding minerals? If so, then the inorganic compounds present may be able to reduce lipids and other complex carbohydrates to molecular carbon and minerals in the form of the biological organism.

So say, for instance, that this organism was suddenly encased in a thick layer of clay. As the review states:

  In clay-rich environments, the large surface area and charge of clay
  grains are thought to contribute to preservation in one of two ways.
  First, enzymes produced either through autolysis or by invading
  microbes are adsorbed to the surface of the clay grains and
  inactivated, slowing or preventing degradation (Butterfield 1990,
  Garwood et al. 1983). Second, molecules directly adsorbed to clay
  grains are resistant to degradation (Stotzky 1980), whereas
  protein-protein layers are readily degraded. This mechanism may
  explain the exquisite preservation of thin carbon films in impression
  fossils such as the feathered dinosaurs of the Jehol Biota (see
  discussion below). As tissues interact with surrounding clay grains,
  only the molecules in direct contact with clays are preserved as
  monolayers, whereas the rest are degraded normally. Thus, surface
  morphology is preserved, and original carbon might be preserved as
  well

Who knows if this process explains these particular fossils. ¯_(ツ)_/¯  As I said earlier, we'd need more information. The section quoted above, though, seems (to me) to provide a plausible hypothesis.

I hope this helps!


Why does pH have an effect on enzymes? I am currently studying biology and would like to know why enzymes work best in a particular narrow range of pH (the so-called pH optimum).

Unlike temperature change, I do not think this has much to do with energy. Do pH-related changes in enzymatic activity have anything to do with the active site?

Proteins are polymers of amino acids. Each amino acid has a side chain. Many of these side chains contain ionisable groups. The ionization state of these groups is dependent on the pH. A group that is protonated at pH=2 and neutral, for example, may become deprotonated at pH=8 and become negative. See the Henderson-Hasselbalch equation.

Protein structure is held together by many intermolecular interactions: dipole-dipole, hydrophobic, electrostatic, etc. The correct protein structure is necessary for function. At different pH levels, the protonation and deprotonation of ionisable amino acids affects the intermolecular interactions within the protein and its conformation will change. At a certain pH, the conformation of the protein will be optimal for its function and this is where it will have maximum activity. As pH deviates to either side of the optimum, the conformation changes and the structure will no longer be correct for proper function.

The ionization state of amino acids is also important in the active site but not only because of conformational changes. Catalytic residues must have certain properties to catalyze their specific reactions. As an example, two Asp residues (which have carboxylates on their side chains) in the active site of DNA polymerase are responsible for coordinating two magnesium ions that promote polymerization. If the pH were to decrease to a point where the Asp residues were protonated, they could no longer bind the Mg2+ ions and the enzyme would not function.


identification of species of snake Can anyone identify this colorful snake found at Pulau Ubin in Singapore?

It is the paradise tree snake (Chrysopelea paradisi). It is a colubrid snake and is common in south-east asia. See this site for a better image.


What is this bug found in a garden in Utah? Apologies for the poor quality of the photo.

I found this bug in a garden in Utah.  The body was flattish, with teal markings (lighter than it looks in the photo) with an interesting pattern of three dots along the back, and a pink cone projecting down to the rear.  It was about the size of my smallest fingernail.

From the searching I've done, the shape and the light "rim" on the outside of the shell look like a June Bug or a Stink Bug, but this one was not as green and the markings seem a lot more pronounced.

Is it a pest to be concerned about?

Based on the pattern of yellow spots it might be a Say Stink Bug.
Check out this list of common Utah stinkbugs

The 12 - 17 mm size is consistent with OP's description and the fact that this insect is often found on ornamental shrubbery is consistent with finding it in a garden.


Why biologic systems tends to become more complex? From elements, chemical compounds, cells, multicellular organisms, society evolves and with each step possibilities increase and things get complex. We are builing structures like ribosome builds polypeptide chains.

So my question is why humans keeps continue to live, does our brain is unconsciously tries to get our society to get bigger, why life has a tendency to get complex with time?

This is an old and interesting question: how do we explain apparent trends in evolution without falling into the trap of teleology or goal-directed evolution, the idea that evolution is working toward a particular end point?

I don't know the answer, and I don't know if anyone knows the answer, but at least two books have tackled the question in a serious way.

John Tyler Bonner argued in a 1988 book that complexity tends to increase because of the correlations between organismal size and complexity. Cosma Shalizi's summmary of his idea is that:

  ... [f]illing a previously empty niche does wonders for the reproductive success of an organism; variations which increase size make new niches available, and so are favorably selected. But, owing to constraints imposed by basic physics and chemistry, larger organisms must be more specialized internally, i.e. more complex, to be as efficient as smaller ones, or even just to survive, so the selection is especially favorable for larger and more complex organisms. Because of the way developmental processes work, this complexity will probably be retained even by later, smaller organisms in other niches. Voila: the evolution of complexity, by means of natural selection.

Bonner's argument might or might not work at the level of cultural evolution.

In contrast, McShea and Brandon argued in a 2010 book that random variation by itself should tend to increase complexity. McShea's summary:

  even when forces and constraints are present, a tendency for complexity to increase is always present. The rationale is simply that when selection is absent, the parts of an organism should tend spontaneously to accumulate variation, and therefore to become more different from each other ... A consequence of the [Zero-Force Evolutionary Law ] is that we do not need natural selection to explain complex tissues and organ in organisms.


What is this New Zealand insect and what is it in? What kind of insect is this?

Found in Early September at Jubilee Park, Dunedin, New Zealand. It was suspended from a silk thread (quite long, a few meters) to a tree above. It was climbing the thread, balling the thread as it went up. It looks like a caterpillar. What species is this and what is it inside of?

The quality of the pictures is not the best one, but due to the fact that this is NZ, it's probably a moth from the species Liothula omnivora.

It's a kiwi insect (that is, endemic to New Zealand). Its English common name is bagworm, and its Maori common name is pū a Raukatauri. The English name explains your question ("what is it in?"). According to Farm Forestry New Zealand:

  The common name of this insect refers to the strong silk bag made as a refuge by the caterpillar. The bag is brown to greyish, often covered with fragments of vegetation, and so tough it cannot be torn open.

Here is a picture of it:

And here is the adult, for comparison:


How protein denaturation affects digestion? Which one of these is a) easier to digest, b) more nutritious (in whatever sense):
1. scrambled egg,
2. raw egg.

Bascially is "denatured protein are worse than not denatured" a myth, or not?

This article specifically looks at the question you're asking.  Just jump down to the conclusion if it's too technical.

To summarize, cooking the egg (or heat pre-treatment as they call it in the paper) leads to a significant increase in protein uptake.

I'd call that myth busted via radiolabeling.


Which of Perutz et al's protein structures other than 3₁₀ helix were correct? In 1950, Bragg, Kendrew and Perutz published "Polypeptide chain configurations in crystalline proteins" (open access) and were famously 'proved wrong' by Pauling, Corey and Branson the following year, in the paper that documented the alpha and gamma helices, "Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain" (also OA)

I'm reading about this (as reviewed here for example) where the idea is that Bragg et al were disproved - in the words of the Pauling paper:

  None of these authors propose either our 3.7-residue [α] helix or our 5.1- residue [γ] helix. On the other hand, we would eliminate by our basic postulates all of the structures proposed by them. The reason for the difference in results obtained by other investigators and by us through essentially similar arguments is that both Bragg and his collaborators . . . discussed in detail only helical structures with an integral number of residues per turn, and moreover assume only a rough approximation to the requirements about interatomic distances bond angles, and planarity of the conjugated amide group, as given by our investigations of simpler substances. We contend that these stereochemical features must be very closely retained in stable configurations of polypeptide chains in proteins, and that there is no special stability associated with an integral number of residues per turn in the helical molecule.

There was one however, the 310 helix which was correctly identified by Perutz's group in 1950. I don't have any access to library facilities at present and online resources aren't quite the same as a solid textbook. I'm wondering if any of the other forms described were in fact correct?

To list, these were:

27a
27b
28
213
214
38
( 310 )
411
413
213

I'll continue looking in the meantime but it's hard to search when there are subscripts in names, and I would think more experienced protein scientists could give me a quicker answer (or just direct me to where I should be reading)

I think you've got the list of good predictions from the Bragg, Perutz, and Kendrick paper.  And the 310 helix was not really right either - it did turn out to show up occasionally in protein structures though.

At the time all of these secondary structure elements were well evidenced from noncrystalline diffraction data and small molecule crystal structures. Examples being collagen from hair and spider silk fiber diffraction patterns. Fiber diffraction of hair, whose ordered structure consists mainly of alpha helices somewhat aligned to the fiber axis (along the length of the hair) or the mainly beta sheets which constitute silk.

Because it was known that these substances contain mainly protein, building models which would show how regular peptide polymers would produce these patterns.  This happened in chemistry and physics departments worldwide.  The paper you cite is representative to the field.

Pauling caused a splash in the spring of 1951 by publishing descriptions of the alpha helix and the beta sheet (both parallel and antiparallel).  The main advantage that Pauling had was that he had studied the structure of simple di-amino acid structures (notably glycyl-glycine) and understood that the peptide bond had some double bond like properties which prevented it from rotating freely.  As the discoverer of valence bond theory, which united quantum mechanics and chemistry and established the basis for at least most organic/biological chemical structures Pauling must have been practically alone in this insight at the time.

This next set the stage for the dramatic race to discover the structure of DNA. If you read Watsons' memoir, he describes how the MRC in Cambridge was still feeling the heat,  competing with CalTech and Pauling.  He and the young lab there was holding their own against the MRC Cambridge with its multiple nobel laureates; a lab which had established the relationship of x-ray diffraction and chemical structure (the notes on chapter 7 are interesting - follow the link).

Looking back on it, Pauling's main advantage was that he understood the peptide bond better than the rest of the world. By the time DNA was being resolved, the conformations of organic molecules were understood by many and the playing field should have been more level.  I'm not sure I buy the arguments that Pauling would have got the structure without seeing the diffraction patterns and even then maybe not. I might not give such strong credence to the idea that Pauling would have gotten the DNA structure so quickly if he had been able to travel.

Of course Perutz and Kendrew verified the peptide alpha helix themselves when they solved the first crystal structures of hemoglobin and myoglobin, having the final say.  The structures contain a small amount of 310 helix but are otherwise full of alpha helices.  I'm not sure that the secondary structure was entirely confirmed until the 1958 when myoglobin was resolved.


Exactly which amino acids are phosphorylated in higher plants during state transitions? I know it is usually stated as the threonine residue near the N-terminus of either light harvesting complex (lhc) b1 or lhcb2, but if this is somehow lost, say in a mutant, is the system flexible enough to compensate by phosphorylation at another site such as a serine residue or will state transitions just cease?

The protein in question from Arabidopsis has this UniProt entry. In the comments you read: The N-terminus of the protein extends into the stroma where it is involved with adhesion of granal membranes and post-translational modifications; both are believed to mediate the distribution of excitation energy between photosystems I and II. As known PTMs we have (see Sequence Annotations) Threonine-38 and Arginine-36; below you can see known mutations. My guess, though, is that they are a few years behind and so it's better to look at recent work.

Let us then take the PMID 11113141 referred to in the above entry and see the citing papers, e.g., via CiteXplore where I see at least a few relevant references on the topic of LHC phosphorylation. If there were a review, it would be listed there. Apparently, there is also a plant phosphorylation site database PhosPhAt which might help, see PMID 22723801.

In summary, not much is known, lacking even a single review on the subject.


Pros and cons of amino acid structure vs DNA sequences for evolutionary comparison This is an analysis question for a lab on the amino acid differences in beta globin amongst different primates, and using such differences to construct a cladogram and infer evolutionary relationships from it. Any input is greatly appreciated!

Question:
What do you see as the strengths and weaknesses of using amino acid structure of proteins for evolutionary analysis? In your opinion, would it be more useful to use DNA sequences for this type of evolutionary comparison between living and extant species? Why or why not?

Amino acid (protein) structure has its advantages over raw DNA.

Protein structure already has introns (noncoding regions) trimmed out which aren't obvious from a plain DNA string.

A protein can have different shapes (such as unbound/bound) or even folded/misfolded (as in the case of prions). DNA doesn't have a way of encoding these changes as they are dependent on substrates, environmental factors and available energy.

Visualizing the 3D structure of a protein can give insight into its functionality that you can't read off a DNA string.


Is this a spider caught on video floating its web between trees? I live in the US and have trail cameras on my property to capture wildlife, visitors, stray animals, etc.  Several are equipped with infrared and I have watched hundreds of hours of video. Many videos feature a large amount of insects flying so I know what a bug looks like on infrared.

What I captured yesterday is completely different. It is a perfectly round sphere floating from one side of my driveway to the other and back again. It appears to me to be on convection currents passing between the trees that line my driveway.

I uploaded this video to Youtube and would be very grateful if you could take a look and tell me if you think it is indeed a spider floating its web between trees. Additionally, are you aware if this phenomenon has ever been captured on video before?  I searched the web looking for other videos but am unable to find any.

The 'orb' appears at 10 seconds into this video.

If you're saying you think this is a spider riding air currents to travel from tree to tree, sorry, but I don't see it. If it's actually moving from one side of the drive to the other, it would have to be moving relatively quickly to cover that distance (about 20 feet according to the video) in only a second or so. If it's just being blown by the air, it seems to me like it would have to have been fairly windy to have moved that quickly, or be capable of directed flight.

It seems more likely to me that's it's just a particle of dust or similar material floating close to the camera. The reflection of the IR light causes it to appear much larger and causes the shape to appear more regular than it truly is. If it's actually a much closer to the camera, only light breeze would be required to show this behavior. There's a strand of web clearly visible near the camera, and perhaps this is indeed something caught in another strand web and dangling down in front of the camera—heck, it could actually be a small spider, but it appears dangling from a web near the camera rather than floating between trees.

I couldn't tell you exactly what it is, but it seems more likely to me that be a trick of light and perspective than a spider floating from one side of the drive to the other.

Disclaimer: I'm not an expert in arachnology or videography. These are just my thoughts on the video.


Skin porosity in glans penis when erect (Apologies if this is a too weird/inappropriate question in this forum. I only thought that I ask it since it happens to be part of human life.)

The skin on a human typically blocks many substances that could be harmful for the organism. One area that is not covered by skin, however, is the "glans penis" (the tip of the penis).

Considering that the surface on this area seems to become more stretched during erection, it would look like erection causes the tip to allow more substances to pass through than otherwise.

Are there any studies about how erection affects the porosity in this area of the body?

So if you're interested in the detailed anatomy of the glans penis, I recommend this as a nice article to go to after you've checked general references.  Opening two sentences are worth quoting here:

  The human glans penis is covered by stratified squamous epithelium and
  a dense layer of connective tissue equivalent to the dermis of typical
  skin. Rete ridges of the epidermis are irregular and vary in height
  depending on location, age, and presence or absence of a foreskin. The
  papillary layer of the dermis blends into and is continuous with the
  deep connective tissue forming the tunica albuginea of the corpus
  spongiosum of the glans penis.

And as pointed out in The Last Word's answer, foreskin covers the penis if you look at humans in an evolutionary scale of time.  The exception being an erection, which should lead to foreskin retraction (at least at some level).

So the question then becomes if the squamous epithelium and connective tissue are more prone to infection than the dermis. First, it's worth pointing out that the epidermis is not equally protective across the body. Think about the skin on your face vs. the bottom of your foot, or vs. a baby's.

I think comparing the glans penis directly to the surrounding tissue -- the prepuce (foreskin), fossa navicularis, and urethra -- makes the most sense. To make a plumbing analogy, is it the pipe (urethra), the fitting (glans penis), hole (fossa navicularis), or insulation (prepuce) that is most prone to infection?

Well, first we need to look at our pathogen, "what's doing the infecting?" For HIV, probably the urethra, but if you're interested in bacterial infection, the best things to look into are balanitis and balanoposthitis.  That would be the inflammation of the glans or glans & prepuce. Here is a good review on infectious causes.

Unfortunately, there is going to a strong sampling bias due to circumcision rates.  Also most studies are not going to be asking the the specific question we are trying to answer here. And it would be hard to prove that infection occurred during the erection, not immediately before or after.

I have found little evidence of bacterial infection of the prepuce but not the glans penis.  I do know of cases of the reverse however, which may indicate that the glans has a greater infection rate.

However, I think it's worth pointing out the difference is not likely to be drastic, and that the surface of glans has many similarities to skin.  For example, it has an epidermis and dermis. It stretches quite well, and I think dryness will be an issue far before porosity.


What is the correlation between hand and neck flexibility? I am trying to understand this statement in the book, Mudras, Yoga in your Hands by Gertrud Hirschi:

  There is a direct relationship between the hands and the neck since the nerve paths run through the vertebral foramina in the arms, hands, and fingers.

Furthermore it is stating that neck flexibility is correlated to hand flexibility.

Where is the vertebral foramina and what is it?

The vertebral foramen

What is it, and what passes through it?

  A number of structures pass through the foramen. These are the root of each spinal nerve, dorsal root ganglion, the spinal artery of the segmental artery, communicating veins between the internal and external plexuses, recurrent meningeal (sinu-vertebral) nerves, and transforaminal ligaments.

The nerves in the hand

  Starting in the trunk of the body, the nerves of the arm and hand arise from the cervical and thoracic regions of the spinal cord as spinal nerves. These nerves merge to form a network called the brachial plexus before continuing into the arm. Five major nerves extend from the brachial plexus into the arm: the axillary, musculocutaneous, median, radial, and ulnar nerves. Each of these nerves carries information in the form of nerve impulses to and from a particular region of the arm and hand. Some of these impulses are sent from various parts of the brain and spinal cord; some come from sense organs located in the joints, ligaments, and tendons; and some come from nervous tissue in the muscles themselves.

In this paragraph it is specifically stated that impulses received in the hand by receptors, can come from the brain and spinal cord "and some come from nervous tissue in the muscles themselves."

The vertebral foramen is a part of the spinal cord, and forms a vertebral canal, the nerves running through it, and the impulses which are sent could be received by the receptors in the hand. Which could affect flexibility in both neck and extremities.

Sources:

https://www.innerbody.com/anatomy/nervous/arm-hand
http://www.emory.edu/ANATOMY/AnatomyManual/38.jpg
http://medical-dictionary.thefreedictionary.com/vertebral+foramen
https://en.wikipedia.org/wiki/Intervertebral_foramina
https://en.wikipedia.org/wiki/Vertebra
http://www.spinalhub.com.au/what-is-a-spinal-cord-injury/what-happens-to-the-spinal-cord-after-injury/spinal-nerves-up-close


Does a DNA sequence has its own derivation tree or pattern? I am new to bioinformatics and natural language processing. In linguistics, they have Treebank - derivation/parse tree for each sentence. For example, a sentence "Sara sleeps" can be visualized by a tree: Sentence -> Subject Verb, Subject -> Sara, Verb -> sleeps.

I've heard about Genbank, a database for nucleotide sequences. Does a DNA has its own derivation tree, or is any pattern in a DNA sequence already known with current technology? I only heard about repeats.

From your example I guess that by "deriving" you mean something like decomposing into elements with diverse functions. Maybe we could apply this concept to DNA sequences: Some parts code proteins, which are decomposed into triplets, each of which codes an amino-acid. Other parts have regulatory functions: They can be motifs not coding a protein, but instead allowing a protein or something else to bind and modify the expression of nearby protein-coding parts. Other parts may contribute to the physical structure of the chromosome, or may have no function at all.


confusion regarding degrees of flexion and a goniometer I have read

https://en.wikipedia.org/wiki/Anatomical_terms_of_motion#Flexion_and_extension

"Flexion ... decreases the angle...Extension is the opposite of flexion, describing a straightening movement that increases the angle between body parts"

I am clear on the directions of flexion and extension

So all agree on direction, but if I look up degrees of flexion, for example

and videos showing usage of a goniometer to measure shoulder flexion, which echo that picture, so 180 degrees is the arm up, and 0 degrees is the arm down.

What I don't quite understand, is that flexion according to wikipedia, should decrease the angle.  Whereas looking at the degrees in that diagram, and in videos of usage of a goniometer, the more flexion you have, the higher the degree.

I can think of two possible resolutions

A) that wikipedia has missed out that in fact, for the case of the arm,  flexion increases the angle. Whereas for bending movement, it decreases it.

or

B) the planes that describe degree of flexion, are different to the ones shown on a goniometer, perhaps, one field uses a gynometer, the other uses a measure with the angles going the other direction

I'm guessing that it's "A" , that wikipedia is misleading and in the case of the "shoulder"(the arm movement considered shoulder flexion and extension), flexion doesn't decrease the angle, it increases it(though wikipedia doesn't say that). But i'd be interested if that can be confirmed.

There are two criteria to differ between flexion and extension:

1) Decreasing or increasing the angle between the involved bones. By this criteria, it should be clear that flexion means bending of the elbows and knees and lateral bending of the spine (the neck and torso) toward the bent side.

2. The anterior/posterior direction of the movement. All anterior (ventral) movements in the neck or torso part of the spine, shoulder, elbow, wrist, fingers, hip, ankle and toes are called flexion and all posterior (dorsal) movements (except in the knee) are called extension.

You should not use the both criteria at the same time, because they can contradict each other.

There are some specifics:

In the wrist, you can have palmar flexion, dorsiflexion (extension), ulnar flexion (abduction) and radial flexion (adduction) (Teachmeanatomy).
In the ankle, you can have plantar flexion, dorsiflexion (extension), inversion (inward rotation, adduction) and eversion (outward rotation, abduction). (ScienceDirect).
In the shoulder and hip, raising a limb to the same side as the limb is, is abduction (lateral extension) and raising it to the opposite side is adduction.
Moving the thumb toward the palm (in the same plane as palm) is flexion (adduction) and moving it away from it is extension (abduction).

You can read about flexion and extension and other movements here: Types of Body Movements (BCcampus)

  Flexion and extension are movements that take place within the
  sagittal plane and involve anterior or posterior movements of the body
  or limbs. For the vertebral column, flexion (anterior flexion) is an
  anterior (forward) bending of the neck or body, while extension
  involves a posterior-directed motion, such as straightening from a
  flexed position or bending backward. Lateral flexion is the bending of
  the neck or body toward the right or left side.

  In the limbs, flexion decreases the angle between the bones (bending
  of the joint), while extension increases the angle and straightens the
  joint. For the upper limb, all anterior-going motions are flexion
  and all posterior-going motions are extension. These include
  anterior-posterior movements of the arm at the shoulder, the forearm
  at the elbow, the hand at the wrist, and the fingers at the
  metacarpophalangeal and interphalangeal joints. For the thumb,
  extension moves the thumb away from the palm of the hand, within the
  same plane as the palm, while flexion brings the thumb back against
  the index finger or into the palm. These motions take place at the
  first carpometacarpal joint. In the lower limb, bringing the thigh
  forward and upward is flexion at the hip joint, while any
  posterior-going motion of the thigh is extension. Note that
  extension of the thigh beyond the anatomical (standing) position is
  greatly limited by the ligaments that support the hip joint. Knee
  flexion is the bending of the knee to bring the foot toward the
  posterior thigh, and extension is the straightening of the knee.
  Flexion and extension movements are seen at the hinge, condyloid,
  saddle, and ball-and-socket joints of the limbs (see Figure 1).

Now, to answer the question about the goniometer.

Again, the confusion about interpretation of this goniometer arises from two different criteria about flexion. The one mentioned in the Wikipedia and other anatomical articles says that in flexion the angle between the involved bones decreases. When you raise your arm, this criteria does not aply because the angle between the bones (humerus/scapula) in the shoulder joint does not really change (unlike in the elbow, for example), so here the criteria that all anterior movements are considered flexion applies. When you have an arm straight down, there is no flexion, so it's considered zero degrees and when it's straight up, it's considered 180 degrees, so the angle is increasing, but this is not an angle between the arm and other bones or the body but between the starting and ending position of the arm.


Does drying meat in the sun make digesting it easier? I was looking into the relationships between man, fire, brain size, evolution, etc. and I learned about other methods of food preparation that eased digestion, but did not use fire. Then, this question popped into my head. Specifically, I am wondering how much easier is sun-dried meat to digest; how much of a benefit is gained in the amount of energy needed for the digestive process?

Various food processing methods, such as cooking, can make meat easier, that is faster, to digest. The purpose of drying meat is to extend its shelf life, not to make it more digestible. Drying removes water from the meat and somewhat physically (but not really chemically) change it.

The amount of calories used for digestion is not that high; probably less than 100 Calories per day, so meat prepared in different ways does not likely significantly affect the amount of calories burnt.


Tools to analyze RNA-seq data I hope this is a good place to ask such question. I have to do some data analysis on RNA-seq data from human cells. I am currently searching for tools to help me with that. Specifically, I would need some tools to analyze the gene expression from the data. Something to help me plot the expression of selected genes in each fastq file and compare the differences in the expression with the possibility to export the results or some command line interface for scripting. Basically I need something where I can put a fastq file and perhaps also a human genome annotation file as input and get gene expression as output. I have looked at bioconductor and it's packages and on Wikipedia's List of RNA-Seq bioinformatics tools. I suppose some of these tools have to be able to do what I need, but I have been unable to find out which one and how should they be used to achieve that. Could someone please give me some advice?

You will likely need a tool to "map" the reads on the reference genome.
You may find such a reference genome, together with annotations, here:
ftp://ussd-ftp.illumina.com/.

Mapping tools such as bowtie2 or bwa take fastq files and reference genomes and output mapping results in a format called sam.

You then have a lot of options to estimate gene expression.

You can write your own algorithm to parse sam format and estimate normalized read counts on each gene.
You can combine more or less low-level tools such as samtools, pysam, htseq with some scripting to do this.
You can use tools that do the counting (like bedtools ot htseq-count) and differential expression analysis (like deseq2).

In the last case, I would advice to start from the documentation of the final tool to find out what are the tools you need to generate the output of the preceding step.

It is very likely you will use some R or Python, or use the web platform galaxy for some of the steps.

Edits

As mentioned by @scribaniwannabe in this answer, the paper about the Tuxedo suite of tools gives a good example of the steps to carry out an RNA-seq analysis using recent tools (as of October 2016).

As @Student T reminds in this answer, RNA-seq data contain reads that can come from exon-exon junctions, so the read mapper has to be set up in such a way as not to discard reads not mapping continuously on all their length on the genome. To my knowledge, HISAT2 and CRAC do this by default. Bowtie2 needs special settings.


If a given DNA oligo is an aptamer, will the corresponding RNA oligo with the same sequence be an aptamer aswell? Functionality of aptamers depends upon the oligo's sequence and secondary structure. So, if I take a DNA aptamer and make an RNA oligo of the same sequence (T replaced with U obviously), will this RNA oligo also act as an aptamer?

There is at least one known case where both the DNA and RNA versions of the same aptamer sequence bind the same target (Lauhon and Szostak, 1995).

But you can't generalize this, there are two differences in structure between RNA and DNA, the Uracil/Thymine change and the missing 2'-OH in DNA. Those differences can affect the binding and overall structure of the aptamer.

It is possible that the RNA version of a DNA aptamer binds the same ligand, but this won't be always the case.


Is there a molecular basis to intelligence? Is there any explanation, gene(s) or whatever detected, that are co-related or explicitly related via mechanical bio-molecular (or at any other level) models that explain the higher or lower intelligence found in different individuals of Homo sapiens?
If so, which and how do they work?

As a Drosophila biologist, I will attempt to address the above question by giving an examples from the Drosophila field. When this paper (http://www.ncbi.nlm.nih.gov/pubmed/7720066) in Cell came out, it sent shockwaves around the world since it showed a molecular mechanism by which production of cAMP and activation PKA, effects CREB transcriptional activation and in turn formation of the long-term memory (LTM) in flies. Some of these CREB over expressing flies could learn a task after simply one try whereas wild-types had to do it several times! This work was later followed by mouse studies (http://www.pnas.org/content/100/18/10518.full.pdf) and comparisons to RTS patients were made. At that time there were discussions of CREB being responsible for intelligence however now there is nice nature review/meta-analysis paper (http://www.nature.com/srep/2014/140225/srep04176/pdf/srep04176.pdf), which says there are no evidence connecting CREB and IQ. This paper performs a literature based investigation and identifies several candidates that are testable and can act as biomarkers for intelligence related therapeutic approach to mental retardation. According to their screen dopamine and norepinephrine pathways seems to be important in IQ-related biological processes.

Hope this helps!


Can CRISPR-Cas9 make changes on a living organism? Can CRISPR-Cas9 make changes on a living organism? What's the limit here? E.g. reversing/restoring hearing loss in a living adult mice.

Answer is yes, but it depends on which kind of phenotype you're going to restore/change. As you can imagine, using crispr cas9 on an high amount of cells require one condition: edited cells need to have a clear advantage in surviving besides the previous.

Here's an example of a crispr-cas9 protocol followed to restore a wildtype phenotype in adult mice.


Identify this roadside plant in Montserrat, Spain Photographed in April; growing abundantly on the side of a rocky path in Montserrat, Spain.  Up to maybe 1 foot (30 cm) in height.

This plant is in the genus Euphorbia, which is a large and diverse group.  The members take wildly different forms, but the general form of this plant is shared by many Euphorbia members.  I'm not sure of the species, but think it is most likely Mediterranean Spurge, Euphorbia characias:

 Photo: Macro63

 Photo: cc-by-sa-2.0 Bernard Dupont.


How does DNA determine all of our hereditary traits? It's my understanding that DNA codes only for protein synthesis. Does that mean that hereditary traits, like the shape of our nose, are determined only by the proportions in which various proteins are synthesised in various parts of our body ?

Does that mean that hereditary traits, like the shape of our nose, are determined only by the proportions in which various proteins are synthesised in various parts of our body ?

Yes, more or less!

A trait that is called heritable is a trait which variance in the population is in part at least explained by genetic variance. Most of these heritable traits, however, are also affected by environmental variation (and other sources of variance). For more information, please have a look at the post Why is a heritability coefficient not an index of how “genetic” something is?

So when you say

  [..] are determined only by the proportions in which various proteins [..]

The term "only" is a bit misleading. Other sources of variance exist that will affect the variance for this trait. However, it is a pretty good approximation to say that the heritable information is conveyed via the transmission of DNA and the phenotypic expression of this DNA is mediated via proteins.

We refer to the DNA -> RNA -> protein having some phenotypic impact relationship by the term central dogma of molecular biology. You might want to read more about it or maybe have a look at an online course such as this one from Khan academy for example. You will want to know the terms translation and transcription.

Now, in reality DNA can affect an individual's phenotype by means other than proteins (or polypeptides to keep it more general) that are synthesized from it. Indeed, many loci (locus=position on a chromosome) affect the expression of other proteins, others are translated into RNA but not transcribed into proteins (e.g. rRNA, tRNA, RNAi, ...) but yet still have an important action on a cell's physiology.


How do viruses such as COVID-9 and flu return in the winter if they disappear in the summer? COVID-19 is gone from the body after a short time, and the maximum time of exposure to showing the symptoms is two weeks. So if no one gets sick for two or three months, how would it return in the winter?

How can it survive so long? Nobody got sick from nowhere except the first one and that things happened once to a lot of years.

I think the first step in answering your question, is correcting part of it. Influenza does not disappear in the Summer. Infection rates decline, but people can still become infected in the off season. Remember, we live in a globally connected society. Summer in the Northern Hemisphere is winter in the Southern Hemisphere. Influenza also has a number of animal reservoirs and intermediate hosts, which can contribute to persistant survival.

As far as the seasonality of infection rates, there are a number of contributing factors. This article from Harvard University discusses a few factors:

  "1) During the winter, people spend more time indoors with the windows sealed, so they are more likely to breathe the same air as someone who has the flu and thus contract the virus.

  2) Days are shorter during the winter, and lack of sunlight leads to  low levels of vitamin D and melatonin, both of which require sunlight for their generation. This compromises our immune systems, which in turn decreases ability to fight the virus.

  3) The influenza virus may survive better in colder, drier climates, and therefore be able to infect more people."

For a more exhaustive discussion of the underlying causes of influenza seasonality, here's an open access review article on the subject.

Some researchers suspect that the SARS-CoV-2 virus, the causitive agent of COVID-19 infections, may have a similar patern of seasonality, but it's probably too early to know for sure how influential each of these factors will be in the long term.


This is probably not a very satisfactory answer. The very next step in Murray's book (3rd Ed) there is a non-dimensionalised version of the model (eq 3.32) which looks like the one given in Boyce's book (10th Ed) except $\epsilon_i$ and $\sigma_i$ (eq 2, Ch 9). If you plug in $\epsilon_i = \sigma_i = 1$ in Boyce's book you get the same fixed point expression (eq 36) as Murray's book.

The idea is: in the RHS of a $\frac{dx_i}{dt}$ term the $x_i x_i$ represents intra-specific interaction and the $x_i x_j$ represents inter-specific interaction between species $i$ and $j$. You can put constants wherever you like to scale these terms with an interpretation. But the qualitative behavior of the system doesn't change and the coefficients persist in algebra, based on how you plugged them.

But to literally interpret the extra factor in the second set of equations: you can think of them like if $a_{ii}$ is the scaling of intra-specific interference, then $a_{ij}$ is a scaling of $a_{ii}$ for inter-species interaction, i.e. the species $j$ interfere with species $i$ with $a_{ij} a_{ii}$.


How does entry of Ca²⁺ to the myocardiocyte make it more contractible? I'm trying to understand why an increase of Ca2+ entering into the cell, increases the force of the heart contractions. Based on what I have watched in many lectures videos on Youtube (this one- "interactive biology" for example on 4:45), Ca2+ basically slows the repolarization in phase II of the action-potential membrane, and I don't understand how it does the cardiac cells more contractible. Or maybe the answer is pinned in the words "typical cardiomyocytes" and then I didn't get it.

The answer is a bit more complex. Calcium ions have a lot of effects in the cardiac myocyte. Apart from the increased contractility (positive inotropy), extracellular calcium concentration also alters chronicity as you mention by altering the rate of repolarisation. An attempt at a simplified picture of the inotropic effects follows:

First is to increase the contractility via directly sensitizing the tropomyosin system. Have a look here. Quoting the paper, "...In both cardiac and skeletal muscle, the force-generating molecular motors (crossbridges) are turned on by increasing the intracellular free calcium level that regulates the troponin-tropomyosin system. However, calcium activation is a two-way process in the sense that activated crossbridges also affect the troponin-tropomyosin system...An increase in Ca2+ activity causes an azimuthal shift of tropomyosin around the filament (by about 30 degrees), thereby increasing the probability of low-force crossbridge interaction, a process which by cooperative effects induces further tropomyosin movement (by an additional 10 degrees) which results in the open state of the filament characterized by forceful cross-bridge interaction...". Hence, higher the intracellular concentration of Calcium, greater is the maximum force.
Sarcomere length also affects the sensitivity to calcium. This increase in contractility is not because of calcium but is mediated by calcium. The reason has something to do with lateral filament lattice spacing decreasing, increasing the probability of cross-bridge formation, increased strain on titin alters lattice spacing and myosin packing.

As I said, this is a bit too oversimplified. There a lot of inter-regulations taking place. Have a look at these papers here.

Myofilament Calcium Sensitivity: Role in Regulation of In vivo Cardiac Contraction and Relaxation (A good review plus a bit of quantification on the topic being discussed)
The negative inotropic effect of calcium overload in cardiac Purkinje fibers (To present the complexity)


What exactly does Curare do to the peripheral nervous system? so, I was told:

  If you give them the right dosage it'll wear off within an hour or two.
  It was used for veterinary stuff until they tried it on a human and realized it only paralyzed you and didn't block the pain. I don't know the exact dosage but if you go over the limit it'll start to relax the lungs
  So the exact dosage will be exactly enough to paralyze them without injury.

SO, naturally, I was wondering, what exactly does Curare do to the peripheral nervous system?

Curare is a plant alkaloid originally used as a poison on darts and arrows used in hunting. It is a competitive antagonist for the nicotinic acetylcholine receptor, which is found in the neuromuscular junction and autonomic ganglia.  We know a lot about this receptor and it's blockade by curare, so most good basic pharmacology textbooks devote a fair amount of space to it and you'll find mention in many physiology and neuroscience textbooks. I'd refer you to Goodman and Gilman Chapter 11 for a general reference.

The basics are as follows:

Curare is a quaternary amine. This means it has a charge on it and cannot cross the blood brain barrier. This was confirmed in 1947 by Scott Smith (pubmed link), an anesthesiologist, who administered very high doses of d-tubocurarine to himself (while under mechanical ventilation), resulting in complete paralysis but no central CNS effects. It's an interesting read if you get the chance, and records very carefully details of the minute by minute response for 4 hours of a series of administrations and reversals (with an acetylcholinesterase inhibitor).

What you get, as reported by Smith and confirmed by others, is blockade of motor outflow with skeletal muscle paralysis (including respiratory muscles) and also probably some ganglionic blockade (this is supported with further research since 1947). There are no changes in sensory inflow or any central effects. The blockade of the nicotinic acetylcholine receptors is reversed with an acetylcholinesterase inhibitor by increasing the amount of acetylcholine in the cleft to the point where it overcomes the competitive inhibition by curare.


Are there any pathogenic archaeans? Most textbooks seems to restrict pathogens to the domains bacteria and eukarya. Are there any pathogenic archaeans?

To date, there isn't a single species that may be considered pathogenic to animals or plants. There are archeon who live in association with animals (in the case of human, they have been found in the gut microbiota aswell as certain skin surfaces) that are mainly methanogens. This could lead to think that archaons could produce "pathologic farting", but that condition has never been described.

In the case of ascidians and other marine invertebrates, some archeon have been found living in symbiosis, with the microbe aiding the animal by means of nitrogen fixation. One could think that, since they're able to live inside the organisms, they could behave as opportunistic pathogens, but none has been described.

Furthermore, it actually exists at least one known species who could be classified as parasitic, the nanoarchaeota Nanoarchaeum equitans, which has been described as a symbiont of some hyperthermophilic archaeon. Despite that description as symbiont, Nanoarchaeum cannot live by its own, while its companion does. Moreover, its genome contains the typical traits associated to parasitism, with great reduction in genome size and loss of many key pathways and cell functions, including methabolic pathways an even some key components of its transcriptional and translational machinery. Since there is no known function of the Nanoarchaeum itself, it should be considered as a parasite.

However, the lack of evidence may be biased, since few people has used metagenomic approach to look for archeon in clinical samples, and some rare cases may be found in the future.


What exactly are computers used for in DNA sequencing? I've thoroughly read the Wikipedia article on DNA sequencing and can't get one thing.

There's some hardcore chemistry involved in the process that somehow splits the DNA and then isolates its parts.

Yet DNA sequencing is considered to be a very computationally-intensive process. I don't get what exactly is being computed there - what data comes into computers and what computers compute specifically.

What exactly is being computed there? Where do I get more information on this?

Computers are used in several steps of sequencing, from the raw data to finished sequence:
Image processing
Modern sequencers usually use fluorescent labelling of DNA fragments in solution. The fluorescence encodes the different nucleobase (= “base”) types (generally called A, C, G and T). To achieve high throughput, millions of sequencing reactions are performed in parallel in microscopic quantities on a glass chip, and for each micro-reaction, the label needs to be recorded at each step in the reaction.
This means: the sequencer takes progressive digital photographs of the chip containing the sequencing reagent. These photos have differently coloured pixels which need to be told apart and assigned a specific colour value.

As can be seen, this (strongly magnified; the image is < 100 µm across!) image fragment is fuzzy and many of the dots overlap. This makes it hard to determine which colour to assign to which pixel (though more recent versions of the sequencing machine have improved focussing systems, and the image is consequently crisper).
Base calling
One such image is registered for each step of the sequencing process, yielding one image for each base of the fragments. For a fragment of length 75, that’d be 75 images.
Once you have analysed the images, you get colour spectra for each pixel across the images. The spectra for each pixel correspond to one sequence fragment (often called a “read”) and are considered separately. So for each fragment you get such a spectrum:

(This image is generated by an alternative sequencing process called Sanger sequencing but the principle is the same.)
Now you need to decide which base to assign for each position based on the signal (“base calling”). For most positions this is fairly easy but sometimes the signal overlaps or decays significantly. This has to be considered when deciding the base calling quality (i.e. which confidence you assign to your decision for a given base).
Doing this for each read yields up to billions of reads, each representing a short fragment of the original DNA that you sequenced.
Most bioinformatics analysis starts here; that is, the machines emit files containing the short sequence fragments. Now we need to make a sequence from them.
Read mapping and assembly
The key point that allows retrieving the original sequence from these small fragments is the fact that these fragments are (non-uniformly) randomly distributed over the genome, and they are overlapping.
The next step depends on whether you have a similar, already sequenced genome at hand. Often, this is the case. For instance, there is a high-quality “reference sequence” of the human genome and since all the genomic sequences of all humans are ~99.9% identical (depending on how you count), you can simply look where your reads align to the reference.
Read mapping
This is done to search for single changes between the reference and your currently studied genome, for example to detect mutations that lead to diseases.
So all you have to do is to map the reads back to their original location in the reference genome (in blue) and look for differences (such as base pair differences, insertions, deletions, inversions …).

Two points make this hard:

You have got billions (!) of reads, and the reference genome is often several gigabytes large. Even with the fastest thinkable implementation of string search, this would take prohibitively long.

The strings don’t match precisely. First of all, there are of course differences between the genomes – otherwise, you wouldn’t sequence the data at all, you’d already have it! Most of these differences are single base pair differences – SNPs (= single nucleotide polymorphisms) – but there are also larger variations that are much harder to deal with (and they are often ignored in this step).
Furthermore, the sequencing machines aren’t perfect. A lot of things influence the quality, first and foremost the quality of the sample preparation, and minute differences in the chemistry. All this leads to errors in the reads.

In summary, you need to find the position of billions of small strings in a larger string which is several gigabytes in size. All this data doesn’t even fit into a normal computer’s memory. And you need to account for mismatches between the reads and the genome.
Unfortunately, this still doesn’t yield the complete genome. The main reason is that some regions of the genome are highly repetitive and badly conserved, so that it’s impossible to map reads uniquely to such regions.
As a consequence, you instead end up with distinct, contiguous blocks (“contigs”) of mapped reads. Each contig is a sequence fragment, like reads, but much larger (and hopefully with less errors).
Assembly
Sometimes you want to sequence a new organism so you don’t have a reference sequence to map to. Instead, you need to do a de novo assembly. An assembly can also be used to piece contigs from a mapped reads together (but different algorithms are used).
Again we use the property of the reads that they overlap. If you find two fragments which look like this:
ACGTCGATCGCTAGCCGCATCAGCAAACAACACGCTACAGCCT
ATCCCCAAACAACACGCTACAGCCTGGCGGGGCATAGCACTGG

You can be quite certain that they overlap like this in the genome:
ACGTCGATCGCTAGCCGCATCAGCAAACAACACGCTACAGCCT
                  ATCCCCATTCAACACGCTA-AGCTTGGCGGGGCATACGCACTG

(Notice again that this isn’t a perfect match.)
So now, instead of searching for all the reads in a reference sequencing, you search for head-to-tail correspondences between reads in your collection of billions of reads.
If you compare the mapping of a read to searching a needle in a haystack (an often used analogy), then assembling reads is akin to comparing all the straws in the haystack to each other straw, and putting them in order of similarity.