5/23/2016

So how exactly is a PCR done?

The sample of interest is first heated to 95°C.

This is done to denature the double stranded DNA to single stranded DNA (bonds are broken).

Then specific known synthetic DNA strands that are 15 to 20 nucleotides long are added to this soup of single stranded DNA.

These are called primers and during this time temperature is lowered to allow or facilitate complementary bonding (if complimentary sequence to the primers exist in the separated DNA strands).

This is the basis for the high specificity of PCR.

If the primers find their compliments, they are called annealed primers.

Then an enzyme called DNA polymerase is added and the temperature of the machine (Thermocyler) is raised to 72°C.

DNA was originally isolated from the bacterium Thermus aquaticus and is thermostable.

This is the step of actual photocopying.

30 to 40 of such cycles when repeated over and over can lead to more than 10^10 amplifications of the starting DNA material which is a colossal number.

End products of PCR assay are seen by subjecting then to electrophoresis on a 2% agarose gel and then staining with dyes like ethidium bromide.

I have been very lucky to have learnt and perform this neat trick at the Wilmer Eye Institute.

Stay tuned to the voice of this storytelling chimpanzee.

Good night mon ami and my fellow cousin apes constituted out of the same genetic code as any bacteria.

5/24/2016

Most people are aware that correction of myopia surgically is done using a specific type of laser called an Excimer (EXited DIMER).

In this procedure, this particular laser removed minute bits of middle layer of the cornea called the stroma.

This tissue destruction is fancifully called ablation. (Doctors and scientists adore fanciful technical terms to add to the sophistication when none is needed).

But even many learned eye doctors would not be aware of tissue sparing Lasik procedure.

How does it differ from the conventional older Excimer stroma ablation?

Well...

The older machines made cylindrical punches of 2 mm diameter circles.

As you can imagine, this left a lot of irregular untreated areas between adjacent laser punches.

To smoothen these irregular left over tissues in order to prevent higher order aberrations (remember the Dutch mathematician Zernike?), these stromal tissues had to be removed.

So not only the amount that was needed to correct the myopia was removed, but also additional planar tissue were removed.

Modern Excimer ablation machines use Gaussian profile (Man, this mathematician Gauss is everywhere) ablations of smaller diameter.

The amount of tissue removed is dramatically reduced.

Today, ablation of about 13 microns of stroma is good enough to correct 1 diopter in the central 6.5 mm optic zone of cornea.

Lots of tissue spared these days by us tissue destroyers.

Stay tuned to the voice of the story telling chimpanzee.

Good night mon ami and my fellow cousin ape evolved with stroma containing collagen matrix in the eyes and everywhere else.

5/25/2016

As we saw earlier, Davisson and Germer were perplexed with the data they were getting from the pattern of electron scattering from the nickel surface.

Yet, they went ahead and published these diffraction curves in the journal Science in 1923.

Even as late as 1926, they had no clue on why they were getting this data.

Those were the ages where the world was still ruled by nationalism, wars, colonialism and racism. 

This also reminds me of Wilson and Penzias who were unable to make the sense of the noise they were getting in the background.

In an extraordinary similarity to the CMB story, Davisson happened to attend a meeting at Oxford in the summer of 1926.

Davisson was surprised to hear Max Born at the lecture using his diffraction curves and data as a confirmation of the de Broglie hypothesis!

What a fascinating moment!

This set his heart beat racing!

Returning to the United States, Davisson made modifications to the tube design and detector mounting.

Then he started applying different voltages to the electron gun, imparting different kinetic energies and momentum to the accelerating electrons.

He got a peak on the detector at an angle theta = 50°, at voltage of 54 V, giving electrons a kinetic energy of 54 eV. 

This he could now explain.

The nickel crystal surface acted like a 3-D diffraction grating.

The angle of maximum constructive interference from an array is given by the Bragg's law (student of Sir J. J. Thomson).

The experimental outcome of Davisson and Germer matched with the predictions and mathematical equations made by de Broglie and Bragg (whose equation I will be sending shortly).

This was the first direct evidence confirming de Broglie's hypothesis.

Davisson's attention to detail, Bell Labs resources for conducting research, expertise of his colleague Germer and luck, all contributed to this experimental success.

Stay tuned to the voice of the storytelling chimpanzee.

Good night mon ami and my fellow cousin ape.

5/26/2016

William Henry Bragg was born in England in the year of 1862.

England by then was a full fledged colonial superpower thanks to the industrial revolution and its naval might. (Remember the Battle of Trafalgar of 1805?).

 (Always remember, those who control the sea trading routes shall rule the world like today's America does and today's China trying to).

At the age of 23 in 1885 William Henry Bragg was appointed the Elder Professor of Mathematics and Experimental Physics in the University of Adelaide.

(Remember that Australia by 1750s was in the pocket of the British Empire even as the empire was losing its North American colonies if you recall my stories on the American Revolution).

Bragg was a skilled mathematician and he had a limited knowledge of physics.

But he was a great lecturer encouraging both the students and teachers.

His interest in physics developed when in 1895 he was visited by Ernest Rutherford, en route from New Zealand to Cambridge; 

This was the commencement of a lifelong friendship.

Friendships are more often built on shared interests and love of subjects and ideas rather than on personalities as I have myself learnt from the few rare precious friends that I managed to make in my life inspite of my taciturn disposition.

Bragg was strongly impressed with the discovery of Wilhelm Roentgen.

On May 29, 1896 at Adelaide, he called the local doctors and gave them a demonstration of "X-rays to reveal structures that were otherwise invisible".

He had used a Crookes tube (remember?) attached to an induction coil and a battery.

Electric spark generated short bursts of X-rays.

Guess what was the subject of the test?

His hand.

Which revealed an old injury to one of his fingers sustained when using a chopping machine on his father's farm in Cumbria, England.

Stay tuned to this story of a very fascinating Englishman in Australia.

Good night mon ami and my fellow cousin ape.

5/27/2016

While in Adelaide, William Henry Bragg reproduced.

Along came William Lawrence Bragg, his son in the year of 1890.

Bragg junior showed an early interest in science and mathematics.

At the age of 5, Bragg junior fell from his tricycle and broke his arm.

His father, Bragg the senior, who was deeply impressed with Roentgen's experiments used the newly discovered X-rays and his experimental equipment to examine the broken arm.

This is the first recorded medical use of X-rays in Australia.

Both father and son returned to England in 1909 where Bragg senior occupied the Cavendish chair of physics in University of Leeds.

Bragg junior entered the Trinity College, Cambridge in the same year receiving a major scholarship in mathematics.

After initially excelling in mathematics, Bragg junior shifted to physics in the later years.

By 1912, when Bragg senior was 50 years old and Bragg junior was merely 22 years of age, both father and son began to work together on a very new field of X-ray crystallography.

Must have been amazing (working next to your own genetically coded product on the same project)!

(Just for your information, their work on proteins and DNA proved critical for the discovery of the structure of DNA in 1953 by Francis Crick and James Watson).

This father and son duo proposed the Bragg formulation of X-ray diffraction in response to their discovery that the crystalline solids produced surprising patterns of reflected X-rays.

More about it later.

Stay tuned to the voice of the storytelling chimpanzee whose DNA was discovered thanks to these unknown X-rays.

Good night mon ami and my fellow cousin ape.

5/28/2016

On November 11, 1912 (the year Republic of China came to be and Titanic sank), William Lawrence Bragg aka Bragg junior, then just 22 years old made a presentation at the Cambridge Philosophical Society.

He explained the results of his X-ray scattering experiments by a crystal.

He did so by proposing a model of crystal as a set of discrete parallel planes separated by a unit distance d.

Now if 2 rays of x-rays are incident at an angle theta, they will have a path difference of 2dsin theta. (U can derive it by simple geometry).

The important thing that I must tell is that the wavelengths of X-rays, and waves of neutrons or electrons are comparable with inter-atomic distance which is around 150 picometre or pm.

Most atoms are between 62 and 520 pm in diameter.

A typical carbon-carbon single covalent bond is 154 pm long.

Wavelengths of X-rays are in the range of 10 to 10,000 pm.

This makes neutrons and x-rays (essentially photons) an excellent tool for probing or investigating atoms.

Now what this Bragg junior stated in that meet is that these 2 rays with a path difference of 2dsin theta will undergo constructive interference if and only if the path difference is either equal to the wavelength or an integer multiple of it.

Now see how mathematics can convert all this to an elegant equation of pithy.

2d sin theta = n lambda

n is a positive integer

all other terms already explained.

Of course, in a real crystal the effect of the constructive (or destructive) interference gets intensified because of the cumulative effect of reflection in successive crystallographic planes of the crystalline lattice.

For this, both father and son were jointly awarded the Nobel prize in physics in 1915 (when the madness and mayhem of the first world war was in full fury).

This has been the only father-son team to jointly win this prestigious award.

Stay tuned to the voice of this storytelling chimpanzee.

Good night mon ami and my fellow cousin ape quite oblivious to his world and happenings of picometre.

5/29/2016

Ernst Abbe was born in 1840 in Germany, the year British Empire pocketed New Zealand and was raging opium war against Qing Empire in China.

His father was a poor man and his schooling was supported by his father's employer.

By the time he finished his schooling, both his scientific talent and strong will power had become obvious.

Despite financial constraints, his father supported his higher education at the University of Jenna and Göttingen (world ranking 100).

While at school, he was influenced by the great mathematician Bernhard Riemann.

At the age of 30 in 1870, he was accepted as an associate professor of experimental physics, mechanics and mathematics at the University of Jenna.

In 1873, just 3 years later, he defined the term:

Numerical aperture (number without any dimension that characterizes range of angles of an optical system).

He also discovered that there is a limit of resolution for any optical system that is defined by the wavelength of wave.

As we saw in the last night bed-time story, to study atoms we need rays of very small length (in picometres).

To study smaller and smaller objects, we need to use light or waves of shorter and shorter wavelength.

A light with a wavelength lambda, travelling in a medium of refractive index n, and converging to a spot with angle theta will make a spit size of radius d such that:

d = lambda/2nsin theta

The term n sin theta is called the numerical aperture (NA).

Hence d = lambda/2NA

In modern optics like our  microscopes, the NA can reach about 1.4 to 1.6.

So the Abbe limit becomes lambda/2.8

Which for a green light of wavelength 500 nm would be 250 nm or 0.25 microns.

This resolution is enough to see most biological cells (1 to 100 microns) but definitely not the atoms (60 to 500 picometre diameter).

This should make u think on the relative sizes of atoms and cells.

Stay tuned to the voice of this storytelling chimpanzee.  

Good night mon ami and my fellow cousin ape.