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Honestly, my blog is a potpourri of biology, medicine, physics, computers and electronics. Loving science as a whole is my strength (and weakness too).

Physiology physics woven fine
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November 26, 2008
12:00 AM
1,163 views

Electron Microscopy And Graphene

by Amiya in Physiology physics woven fine

Richard Feynman onced remarked that there's plenty of room at the bottom. Indeed, with the aid of electron microscopy and nanotechnology we have realized this. Here, the mechanisms of electron microscopy and its much awaited substrate, 'graphene' is discussed.... Read more »

John Silcox. (2008) Microscopy: Spot the atom. Nature, 454(7202), 283-284. DOI: 10.1038/454283a

November 20, 2008
02:00 PM
1,150 views

Hearing Involves Sound Physics

by Amiya in Physiology physics woven fine

The way we hear sound is complex. The different attributes of sound (namely, intensity, frequency, the direction from which it is coming etc.) are faithfully perceived in the auditory cortex. The whole procedure may seem rather straightforward, but it is far more complicated than what looks so deceptively simple.The sound waves (say from an orchestra) impinge on our eardrums. Sound waves are mechanical waves consisting of condensation and rarefaction, things we learned in our school days. These waves then vibrate our eardrums (Tympanic Membrane; TM). The vibrating TM then transfers its mechanical energy to the oval window, in the membranous labyrinth of the cochlea, via an ossicular chain consisting of three (3) very small bones.The membranous labyrinth consists of three adjoining tubes coiled side by side (as shown in the figure). If we were to make a section through it, we would find 3 separate compartments within it: Scala vestibuli, Scala media and Scala tympani. Scala vestibuli is connected to Scala tympani at the apex of the cochlea, a place called helicotrema. While Scala tympani contains a fluid called endolymph (a fluid rich in K+ or potassium ions); the other 2 tubes contain perilymph (a fluid very similar to plasma, rich in Na+ and low in K+).As the oval window vibrates, the fluid in Scala vestibuli (perilymph) also vibrates. Sound was traveling in air before it struck the eardrum, but here, we see that they are now propagating in a fluid medium, which has far more inertia than air. The possible impedance mismatch that would happen is compensated by the eardrum itself and the ossicular chain. The lever system of the ossicular chain amplifies the force of sound waves about 22 times, so that the total force at the oval window is 22 times than what the TM experienced originally.Now, vibrations have set up in the Scala vestibuli form the oval window. These vibrations find their way to the Scala media, as the two tubes are separated by only a very thin membrane (Reissner’s membrane). Hence, fluid in the Scala media (endolymph) vibrates whenever the oval window is vibrating.The vibrating endolymph sets up a wavy motion in the basilar membrane (BM). The ‘real analysis’ of sound waves starts here! The BM performs real time spectral analysis of sounds it is presented with (analysis of frequencies below 200Hz is skipped though). We normally hear in the frequency range of 20Hz to 20 kHz.The hair cells in the organ of Corti, our hearing apparatus, are arranged in such a manner along the BM that those near the base of the cochlea will respond to high frequencies; while as we go up to the apex of the cochlea, the BM reacts best at low frequencies. In other words, each part of the BM has its own unique maxima, the frequency at which the BM responds most well. Below 200Hz, there is no such place encoding.Our ears follow another principle. The ‘traveling wave’ spreads quicker near the base of the cochlea and its speed diminishes fast as it goes up. This ensures that a longer stretch is available for the higher frequencies; else the higher frequency part would have been bunched together, creating a loss in the HF range. This non linearity in traveling wave propagation is thus needed.Generator PotentialThe genesis of generator potentials in the hair cells is also interesting. Imagine that a group of persons of varying height are standing on a carpet. A thread is attached from the top button (of his shirt) of the smaller person to the top button of his taller counterpart. If the carpet is now tilted by pulling it up from the short person’s end, the thread will now be stretched snapping the taller person’s button. The hair cells also have threads (Tip Links) extending from shorter to their taller cousins. A traveling wave will cause pulling of tip links, resulting in the opening of a mechanically sensitive cation channel. Since potassium is the predominant cation in the endolymph, K+ will then enter the taller hair cells, creating depolarization.Frequency DiscriminationWhen we listen to music, our ears pick up the frequencies in a number of ways. Firstly, the place on the BM where maximum excitation takes place is actually a function of frequency. As a matter of fact, there is a frequency map along the BM. Secondly, at frequencies below 3 kHz, the nerves fire in synchrony with the incident sound waves. This is called the ‘volley principle’. The ‘phase locking’ of the two frequencies that occurs below 3 kHz, is highly analogous to the ‘phase locked loops’ in electronic circuits (NE565). Thus ‘volley principle’ allow us to discriminate frequencies. Actually, volley effect is more important in ‘loudness’ assessment. ‘Pitch’ (the subjective/psychological dimension related to frequency) can also be moderated by factors such as loudness and the duration of sound. At low frequency (below 500 Hz) pitch seems lower and at higher frequencies (above 4 kHz) pitch seems higher, as the loudness increase, when the frequency is kept constant. Again, when the duration of sound increase from 0.01 second to 0.1 second, the pitch will rise too, for a particular frequency. Sound of less than 0.01 sec duration does not evoke appreciation of any pitch by us.Loudness DiscriminationLoudness is the perceived intensity of sound, a subjective psychological dimension. The interpreted sound sensation is proportional to the cube root of the actual sound intensity. As such, the ear works at the top of its limit, at a point analogous to Hopf bifurcation, beyond which instability in oscillations occur.As the sounds become louder, the amplitude of BM movement is more, resulting in more excitation of hair cells. Secondly, with greater loudness, the hair cells around the ‘maxima’ fire too. This causes spatial summation. Thirdly, the outer hair cells are stimulated at loud sounds. The brain will automatically infer loudness levels when cells corresponding to the outer hair cells fire.Locating SoundsThen there is location of the direction of sound. We can locate whether the drums are on the left and the lead guitar is to the right. This is achieved by calculating which ear gets the sound first (time lag) and/ or which ear gets it louder (intensity). The time lag method works below 3 kHz; while intensity method works at higher frequencies.Front/ back discrimination is done by the pinna (auricle) of our ears due to their particular shape.Auditory nerveIt is interesting that each auditory nerve fiber has its own characteristic frequency, the frequency at which it responds most well. However, it is true only at low intensity. At higher intensities, this specificity is lost and they then respond to a wider spectrum of frequencies. The auditory nerve produces a flurry of action potentials, the frequency of which depends on the intensity of the sound stimuli, it is exposed to. This is very much similar to ‘voltage to frequency converter’ ICs (LM331 is one such VFC IC), where a change in voltage at the input of VFC will cause a change in frequency at the output.The auditory nerve then goes to the: cochlear nucleus in the medulla--Superior olivary nucleus--Inferior colliculus (via lateral lemniscus)--Medial Geniculate Body (in the Thalamus)--Auditory cortex.The nerve synapses with higher order neurons in the above places, which then relay to the nerves upstream. Everywhere in its course, including the nuclei, there are clearcut ‘tonotopic maps’, representing definitive frequency layouts. There are also extensive crossing of nerve fibers to the opposite side. Before the fibers reach the auditory cortex, they connect to many reflex pathways vital to life.The auditory cortex (Brodmann’s area 41) is the portion of the cerebral cortex in the superior temporal gyrus. Its anterior part is mainly concerned with low frequency and the posterior part tackles the higher frequencies. Thus area 41 also has its own tonotopic map. Secondary auditory cortex (auditory association area) is vital for the interpretation of sounds. A person, in whom Wernicke’s area (part of auditory association area) is damaged, will hear normally but will fail to understand its meaning, leading to aphasia.The sheer complexity of the auditory circuitry is really mind-boggling: the logarithms (we hear in a log scale, not a linear one), cube functions, phase locking are only some of them. The range of sound intensity (from whisper to the roar of a jet plane) we hear is about 1 trillion fold; but surprisingly, the auditory nerve fibers have a much less dynamic range. Yet we hear the full range. It’s really amazing.P. Martin (2001). Compressive nonlinearity in the hair bundle's active response to mechanical stimulation Proceedings of the National Academy of Sciences, 98 (25), 14386-14391 DOI: 10.1073/pnas.251530498Last modified: neverReference: Textbook of Medical Physiology, 17e, Guyton and Hall... Read more »

P. Martin. (2001) Compressive nonlinearity in the hair bundle's active response to mechanical stimulation. Proceedings of the National Academy of Sciences, 98(25), 14386-14391. DOI: 10.1073/pnas.251530498

November 26, 2008
12:00 AM
1,139 views

Neural Networking, Alzheimer's Disease and Memory Share a Few Things

by Amiya in Physiology physics woven fine

In the hippocampus, the part of brain that processes memory, has a neural architecture that resembles Hopfield network of artificial intelligence. This LAN like architecture is synchronized with cues from within the brain and outside. The brain thus has some similarities with information theory.... Read more »

E . Menschik. (2003) Neuromodulatory control of hippocampal function: towards a model of Alzheimer''s disease . . Artificial Intelligence in Medicine, 99-121.

December 9, 2008
02:44 PM
1,104 views

Fantastic Fluorescence:Brainbow and The Nobel Prize 2008

by Amiya in Physiology physics woven fine

In my childhood, I used to be fascinated by the mysterious glow of fireflies. Later I learned that it was due to a reaction between a substance called Luciferin and an enzyme, luciferase, a phenomenon called bioluminescence. This kind of glow is not limited to land creatures. Creatures living at the bottom of oceans too emit light.Osamu Shimomura of Japan was given the task of isolating the substance which let the marine mollusk Cipridina glow when it was crushed and mixed with water. He succeeded, and on the wings of his publication, was recruited by the Princeton University, in the United States. There he began studying Aequorea Victoria, a marine jellyfish which glowed green when agitated. The jellyfish had an umbrella like shape and its outer rim glowed green. He chopped off the outer edges, crushed it, and filtered it to obtain a ‘squeezate’. He noticed one day that the ‘squeezate’ glowed blue when he poured some into the sink. He understood that it was the calcium ions (Ca++) in the seawater present in the sink that made it glow blue. It was christened aequorin.During the extraction process they also chanced upon another protein called GFP, for green fluorescent protein. It glowed green when excited with ultraviolet light or light in the blue spectrum. The structure of GFP is barrel shaped (also likened to beer can shape), and consists of 238 amino acids. The chromophore or light emitting part is in the interior of the ‘beer can shaped’ molecule, in a region called the alpha helix region (of the molecule); while the exterior of the molecule was comprised of beta pleated sheets of the GFP molecule. Shimomura and colleagues showed that the blue color emitted by aequorin donor excited the GFP acceptor in an energy transfer process. The photons in the blue wavelength were absorbed by the GFP chromophore and photons of green wavelength were emitted - a phenomena called (bio)fluorescence. Fluorescence differs from luminescence from the fact that in fluorescence light of another wavelength is emitted than the one absorbed and luminescence means emission of light.The whole story struck a chord in Martin Chalfie’s ears. He thought what if he could harness the gene that codes for GFP and bind it to the segment that coded for a protein of interest? He worked with a roundworm, Caenorhabditis elegans, a simple organism with only 959 cells and yet a complete organism for it could procreate, had a brain and even one third of its genes were related to humans. It was translucent and hence studying its interior was easier. He contacted Douglas Prasher who was also hot in the trail for the GFP genes. Douglas Prasher did as he promised. He sent the GFP gene to Chalfie once he got hold of the gene. Chalfie introduced it behind the promoter of the gene that coded for proteins in C elegans’ touch receptor neurons. The neurons were cleanly delineated, that too in a live worm and ‘real-time’! GFP, being a natural gene product, is non toxic.Roger Tsien wanted more. He knew from earlier studies that the ‘chromophore’ had 3 key amino acids: serine, tyrosine and glycine in position 65, 66 and 67 respectively in the 238 amino acid long GFP molecule which formed the chromophore. He used DNA technology to alter the amino acid sequence so as to obtain GFP variants that would absorb and emit light in different part of the electromagnetic spectrum. This way he obtained cyan, yellow and blue. He obtained DsRED, a red GFP-like protein extracted from coral, from two Russian researchers and modified it so that it was stable and of desired molecular weight.It was all set by now. Researchers now modified mice genetically and introduced the gene for red, cyan and yellow GFP. They expressed the corresponding proteins in their brain and what we got is a riot of colors, the ‘brainbow’, short for brain and rainbow. Like the elementary colors, these colors when combined in different proportions, produce many colors, just as a color printer does using them (cyan, yellow and red). One could now visualize the neural circuitry in much the same way as seeing electronic circuits. Disease detection and progression in Alzheimer’s disease, cancer and Parkinson’s disease are some potential clinical applications. Watching biogenesis of HIV1 (the virus that causes AIDS) in live cells in real time is now an easy meat. GFP can also be engineered to recognize heavy metals like cadmium (a cancer causing chemical), explosives like TNT and Arsenic (a water pollutant causing Arsenicosis).Osamu Shimomura, Martin Chalfie and Roger Tsien were awarded the Nobel Prize in Chemistry, 2008. Sadly, Doug Prasher was left out, despite his outstanding contribution in this field. He is now driving a van at $10 an hour to meet his living expenses. He is not alone. This year’s Nobel in Physiology or Medicine too left out Robert Gallo, an HIV pioneer. So, not totally a happy ending.Last modified: neverReferences:The Nobel Prize in Chemistry 2008The Man Who Missed the Nobel PrizeStuart Cantrill (2008). Nobel Prize 2008: Green fluorescent protein Nature Chemistry DOI: 10.1038/nchem.75... Read more »

Stuart Cantrill. (2008) Nobel Prize 2008: Green fluorescent protein. Nature Chemistry. DOI: 10.1038/nchem.75

November 26, 2008
12:00 AM
1,086 views

Molecular Basis of Genetic Switch In The Circadian Clock

by Amiya in Physiology physics woven fine

The circadian clock keeps time by switching on and off a genetic switch. The intricacies of the master clock in the hypothalamus is described here.... Read more »

J.-C. Leloup. (2003) Toward a detailed computational model for the mammalian circadian clock. Proceedings of the National Academy of Sciences, 100(12), 7051-7056. DOI: 10.1073/pnas.1132112100

January 11, 2009
02:06 PM
1,079 views

Visualizing Viral Kinetics Using Fluorescence and Bioluminescence

by Amiya in Physiology physics woven fine

It would be nice if we could see an individual virus particle, a virion, in real time within a mammalian tissue starting from its attachment to the host cell and entry, to its assembly and budding and release. The dynamics of viral production has been studied using computational models by noting the response of the virus to exogenous administration of reverse transcriptase and protease inhibitors. It was noted that a mind boggling 10^10 to 10^11 virions are produced each day by using this mathematical model. Now, Jouvenet et al have been able to fluorescently label a molecule called Gag protein (for group specific antigen), the major structural component of HIV. With the aid of fluorescence resonance energy transfer (FRET) and other techniques on these fluorescently tagged virions in living cells, they have been able to see the biogenesis of HIV virions in real time; from viral assembly to release by budding. The assembly rate accelerated as the Gag protein accumulated inside the cells. Typically, the time required for the assembly was just 5-6 minutes.In fluorescence resonance energy transfer (FRET), an external light source shines on a donor fluorescent molecule. The donor molecule gets excited and emits light of a different frequency (fluorescence), which activate the acceptor molecule. The acceptor fluorophore then emits a photon of yet another wavelength (or a quantum, as we are referring to the particle nature of light here). Both donor and acceptor fluorophores are nothing but color variants of green fluorescent protein or GFP. The whole process (FRET) is noisy as the incident light messes up with the emitted light. The incident light may also activate the acceptor fluorophore directly, leading to error.Recently, Asokan et al used bioluminescence from Gaussia luciferase to study adeno associated virus (AAV) kinetics in living mammalian cells. By using bioluminescent molecules, the external light source as used in FRET was no longer needed. This way, direct activation of acceptor molecule was avoided and background noise was kept to a minimum. They first amplified gLuc (Gaussia luciferase) in a plasmid by polymerase chain reaction or PCR, using primer sequences. They then fused the resulting protein to that of an adenoviral subunit of AAV, called Vp2. The resulting gLuc/AAV construct was then injected into the left hind limb of rats. They could clearly notice the AAV vector dynamics. The importance of such dynamics is realized when the use of AAV as a vector in gene therapy is considered. They opined that such a technique would be ideal in studying viral dynamics in peripheral tissues such as the eye and the brain.Bioluminescence is used to study virus tropism and viral kinetics. Tropism refers to the different populations of host cells a virus can attack. Retroviruses have a narrow tropism meaning they can infect only a few types of cells such as CD4+ T cells and macrophages. Previous studies employed Gaussia luciferase reporter gene as a tool for studying viral dynamics. Recent experiments promise a better future for the study of viral behavior.References: A Asokan, J S Johnson, C Li, R J Samulski (2008). Bioluminescent virion shells: new tools for quantitation of AAV vector dynamics in cells and live animals Gene Therapy, 15 (24), 1618-1622 DOI: 10.1038/gt.2008.127Human Immunodeficiency Virus Disease: AIDS and Related Disorders: Anthony S. Fauci, H. Clifford Lane, Harrison’s Principles of Internal Medicine, 17th Ed.Imaging the biogenesis of individual HIV-1 virions in live cellsNolwenn Jouvenet, Paul D. Bieniasz, & Sanford M. SimonLast modified: never... Read more »

A Asokan, J S Johnson, C Li, & R J Samulski. (2008) Bioluminescent virion shells: new tools for quantitation of AAV vector dynamics in cells and live animals. Gene Therapy, 15(24), 1618-1622. DOI: 10.1038/gt.2008.127

November 26, 2008
12:00 AM
1,028 views

Scientists Simulate Learning In Amoeba Using Memristor

by Amiya in Physiology physics woven fine

Amoeba, a unicellular organism, learns and remembers from environmental cues such as temperature variation. This 'cognitive' behavior of amoeba has been simulated in an electronic circuit, employing a brand new 'passive' electronic component called 'memristor'.... Read more »

Tetsu Saigusa, & Yoshiki Kuramoto. (2008) Amoebae Anticipate Periodic Events. Physical Review Letters, 100(1). DOI: 10.1103/PhysRevLett.100.018101

November 26, 2008
12:00 AM
1,028 views

Smelling The Intentions Of Olfaction

by Amiya in Physiology physics woven fine

Olfaction or smelling is rather fishy. It is important to life; and for Toxoplasma gondii, to propagate their species. In humans, surprisingly, it bypasses the thalamus, unlike other sensations which obediently pass through it. Theres even a quantum touch to it!... Read more »

Jennifer C. Brookes, Filio Hartoutsiou, A. P. Horsfield, A. M. Stoneham. (2006) Could humans recognize odor by phonon assisted tunneling?. arXiv:physics/0611205v1 .

September 7, 2008
11:33 AM
995 views

Learning Memory Lessons From Aplysia

by Amiya in Physiology physics woven fine

While you are reading this on your computer, there may be many distractions in the background. Your mom may be shouting at someone or your daughter may be receiving her piano lessons. But after you finished reading this, no memory trace of this background remains. They are not registered with your memory. We seem to ignore this 'negative memory' by a process called 'habituation'. We remember by consolidating memories by another process known as 'sensitization'. But what is this that we call memory? Memory helps us to store, retain and retrieve information. To start it all, learning is needed.Now you might ask why Aplysia out of all animals? Aplysia californica, called 'sea hare' by the ancient Greeks, is a marine snail which has some resemblance to a rabbit. A hermaphrodite by sexual orientation, Aplysia feeds on marine algae, and often takes the color of the algae that it eats. When threatened, it liberates a colored, irritant compound to blind the attacker, as seen in the left. It was Eric Kandel who used this phenomenon to study how neural transmission occurred through synapses. He was awarded the Nobel Prize in Physiology or Medicine in 2000 for his pioneering work on Aplysia. Aplysia offers a distinct advantage by: 1. eliciting a visible (measurable) response (siphon-mediated gill withdrawal reflex) to a stimulus, that can be studied directly; 2. the response is triggered by several electrical synapses firing simultaneously, exemplifying several output in response to a single input; 3. Smaller number of neurons, about 20,000; 4. BIG neurons. Hence this animal is considered a role model in neurobiology.The organism can be stimulated by the application of a minor electric shock to one side of the siphon, and the magnitude of response can be measured by a force transducer, a device, usually piezoelectric, which converts mechanical pull in terms of electricity. Applying a more intense shock to the tail, or administration of chemicals into its abdominal ganglion are other ways of stimulating the mollusk. After careful observations, scientists postulated that habituation, sensitization and classical conditioning were responsible for the learning that occurred in Aplysia.In the picture on the left, you can see a presynaptic neuron on the left side, a postsynaptic neuron on the right and another neuron (facilitator terminal) on top left stimulating the presynaptic neuron. The flow of impulse propagation is from left to right, that is, from presynaptic to postsynaptic neuron. When the presynaptic neuron was stimulated alone, the post-synaptic neuron responded in a ‘what is it’ response. When the stimulus was given repeatedly, then the response of the post-synaptic neuron became less and less. This implies that the post synaptic neuron became as if ‘habituated’. On the other hand, when a noxious stimulus was applied at the ‘facilitator terminal’ at the same time the presynaptic neuron was stimulated, the response became stronger and stronger. They called this ‘sensitization’.In the case of habituation, it was found that the release of neurotransmitter diminished in the presynaptic neuron, possibly due to progressive inactivation of calcium ion channels. It is the calcium ion channel which allows degranulation and release of neurotransmitters. Thus inactivation means blockage of impulse. Structurally, both the presynaptic vesicle number and size are seen to decrease in habituation.In sensitization, both the presynaptic vesicle number and size increase. Here the ‘noxious stimulus’ delivered alongside, causes release of serotonin from the facilitator terminal. This chemical, also called 5HT, binds with 5HT receptors in the presynaptic terminal. This is followed by activation of an enzyme known as adenylyl cyclase, which in turn produces cyclic AMP from ATP. cAMP then activates another enzyme, protein kinase A (PKA), which phosphorylates potassium ion (K+) channels. As a result K+ channels get blocked. When an imulsee arrives at the synapse, the membrane gets depolarized, i.e., the inside of the cell becomes positive with respect to the outside. For the cell voltage to return to its normal polarized state, the potassium ions must diffuse out, through K+ channels. But the exit route is blocked now. The action potential remains longer; more Ca++ enters into the presynaptic terminal.Recent evidence points at the role of post synaptic neurons in habituation, sensitization and classical conditioning. Glanzman et al have proposed that activation of postsynaptic glutamate receptors might play a critical role in mediating long-lasting habituation of gill withdrawal reflex in Aplysia. A whole new range of activity starting at the synaptic knob to the nucleus and thence back to the knob again has been proposed for memory storage.Short-term memory, which usually lasts for a few minutes, involves covalent bonding of pre-existing proteins leading to alterations in the strength of already existing connections. By contrast, long-term memory requires mitogen activated protein kinase (MAPK), CREB and new mRNA and protein synthesis; in addition to PKA.MAPK migrates into the nucleus where it phosphorylates cAMP-responsive element binding protein (CREB). This then regulates gene expression, resulting in transcription and translation. Moreover, long-term memory is associated with the growth of new synaptic connections, phosphorylation of post synaptic densities (PSD is like a scaffold on which proteins are assembled) and many other processes. Thus it seems post synaptic mechanisms might have a bigger role than imagined.So far, we discussed about only one form of memory: implicit or non-associative memory. Declarative or explicit memory consists of semantic (book) and episodic (related with places, memory of events) memory, which are consciously stored. Humans are perhaps, the best or only known subject in this regard. We certainly can't expect Aplysia to speak out.Last modified: neverReferences:Prolonged Habituation of the Gill-Withdrawal Reflex inAplysia Depends on Protein Synthesis, Protein Phosphatase Activity, and Postsynaptic Glutamate ReceptorsYoussef Ezzeddine, David L. GlanzmanMolecular Mechanisms of Memory Storage in AplysiaRobert D. Hawkins, Eric R. Kandel and Craig H. BaileyC. Bailey, M Chen (1983). Morphological basis of long-term habituation and sensitization in Aplysia Science, 220 (4592), 91-93 DOI: 10.1126/science.6828885... Read more »

C. Bailey, & M Chen. (1983) Morphological basis of long-term habituation and sensitization in Aplysia. Science, 220(4592), 91-93. DOI: 10.1126/science.6828885

May 8, 2008
12:00 AM
981 views

HistoMag: Nanomaterials in Medical Physics

by Amiya in Physiology physics woven fine

Long ago when I used to be a medical student, my Anatomy teacher said that the breasts were an ornament to a lady and it gave motherhood to a woman. The words still reverberate in my ears. This aesthetic organ is frequently targeted by cancer. Put in other way, cancer of the breast is the second most common cancer worldwide (lung cancer tops the list) among both the sexes, and the most common type of cancer in women.Diagnosing cancerous cells have been a nightmare for pathologists. We can not define a normal cell properly and differentiating them with cancerous cells can be pretty tough. Apart from their detection by radiological investigations which include X-rays, CT scan, MRI and other imaging modalities; we depend heavily on tissue biopsy samples collected from the patient's suspected specimen. We then stain the specimen using various dyes and examine them under the microscope.For example, in the above picture, a section of breast tissue has been stained with immunoperoxidase. Such staining employs targeting and latching onto a tissue antigen of interest by using an external antibody (the immuno part), and then making these tissue antigens visible by the formation of a colored product by catalytic reactions brought about by peroxidase.Now scientists have gone one step further. In some cancers of the breast there is an overexpression of a protein (antigen) called HER2/neu (Erb B2). This is a transmembrane protein, meaning that this molecule has an extracellular domain, a membrane spanning portion and an intracellular part. The peculiar nomenclature derives from the fact that this molecule is in fact a receptor for human epidermal growth factor and was found in rat neuroblastoma cell lines. Surprisingly, HER does not seem to have a physiological ligand, making the receptor look like a lady who does not have a mate! The protein when over-expressed, may form complexes among themselves, thereby transactivating its inherent tyrosine kinase activity. Unleashing the tyrosine kinase activity results in a cascade of activity that fosters tumorigenesis (picture on the left).Scientists are now tagging magnetic nanoparticles with antibody to HER2/neu. Trastuzumab (herceptin), as the antibody is known, is a humanized monoclonal antibody (only one type/clone of molecule). Thus magnetic nanoparticles attaches to HER proteins (via trastuzumab); the density (intensity) of which can then be probed by applying the specimen to a magnetic field and extrapolating the the distortion these nanoparticles induce in them. Researchers at University College London (UCL) in the UK have developed HistoMag system which uses this technology. A drive coil (picture shown) produces a magnetic field which is made to vary with time, and a magnetometer using SQUID (superconducting quantum-interference device) as the pick up coil. The tissue section was sandwiched in the middle. Apart from detection of malignant cells it is also capable of predicting what population of women are likely to benefit from Herceptin (Trastuzumab) therapy. (In passing, it may be said that the same magnetometer device is being developed further so that it may, one day be able to pick-up your thoughts non invasively.) Many different approaches are cropping up which use nanotechnology, optical imaging and other modalities for the imaging of tissue sections. Quentin Pankhurst, professor of physics at UCL, the man behind HistoMag, has previously developed and commercialized SentiMag, a device which detects sentinel lymph nodes (lymph nodes first to enlarged in cancer).In another development, researchers at the University of Debrecen, Debrecen, Hungary and Max Planck Institute for Biophysical Chemistry, Göttingen, Germany, have used paramagnetic microspheres coated with ligands (Herceptin) to attach to HER2. They then used confocal laser microscopy and digital image processing to 'see' the trans-activation (of ErbB2 (HER-2)). In confocal laser microscopy, a laser light is thrown into the sample through a special dichroic mirror, which allows light of one (long) wavelength to pass and that of other (short) wavelengths to reflect. When a laser of blue color (say) strikes the sample, which has been treated with a fluorescent dye, light of another wavelength say green is emitted. The dichromatic mirror now filters the blue light, while letting the green light pass, which is then amplified by photomultiplier tube and visualized. They found this to be an efficient tool in assessing Erb (HER2) activation, signal propagation and heterodimer formation. In vivo neoplasms may be imaged by administering the patient a dose of these nanomagnets by mouth or by injection, and then imaging the patient. A modification of the device will be necessary.Friedländer, E., Arndt-Jovin, D.J., Nagy, P., Jovin, T.M., Szöllősi, J., Vereb, G. (2005). Signal transduction of erbB receptors in trastuzumab (Herceptin) sensitive and resistant cell lines: Local stimulation using magnetic microspheres as assessed by quantitative digital microscopy. Cytometry Part A, 67A(2), 161-171. DOI: 10.1002/cyto.a.20173Last modified: neverReference: hyper-links, unless otherwise mentioned... Read more »

Elza Friedländer, Donna Arndt-Jovin, Péter Nagy, Thomas Jovin, János Szöllősi, & György Vereb. (2005) Signal transduction of erbB receptors in trastuzumab (Herceptin) sensitive and resistant cell lines: Local stimulation using magnetic microspheres as assessed by quantitative digital microscopy. Cytometry Part A, 67A(2), 161-171. DOI: 10.1002/cyto.a.20173

November 26, 2008
12:00 AM
956 views

Unlearning Memories: You Have Been Erased!

by Amiya in Physiology physics woven fine

Memories, even long term ones, can be effaced. Giving electroshock or anesthetics immediately after someone has learned a procedure rob off memory 'formation'. But some oligodeoxyneucleotides and other drugs can 'erase already etched' memories that were thought to be rather permanent.... Read more »

C. K. McIntyre. (2005) Memory-influencing intra-basolateral amygdala drug infusions modulate expression of Arc protein in the hippocampus. Proceedings of the National Academy of Sciences, 102(30), 10718-10723. DOI: 10.1073/pnas.0504436102

January 19, 2009
08:05 AM
952 views

Phase Alignment of Neocortical Gamma Oscillations by Hippocampal Theta Waves

by Amiya in Physiology physics woven fine

An empty brain is the devil’s workshop, goes the proverb. Actually, the brain is never empty. Even in our deepest slumber, the brain continues to weave waves of electrical rhythms that can be seen with the aid of electroencephalogram or EEG. When we place electrodes on the scalp or on the cortex (inside the skull), and amplify the faint signals via bioinstrumentation amplifier, we can lay our hands on these fluctuating rhythms. (More on the electronics of EEG may be found at the OpenEEG project site).We have as many as 100 billion neurons in the brain. In the superficial layers of the cortex, the neurons have numerous dendrites branching out from the soma or cell body (shown in grey oval in this picture).These neurons have been compared to a forest of trees where the branches are the dendrites and the trunk the axon. These dendrites make extensive connections among each other. They also get connections from the axon collaterals of neighboring axons (i.e. the 'trunks' of other trees connect to these 'twigs' by offshoot from the trunks). Since there are a lot of axons converging on the dendrites of each neuron, and given the fact that these axons can be excitatory (red) or inhibitory (green) depending on the neurotransmitter, the sum of input may be either negative or positive (with respect to the cell body). Thus an alternating current (cortical dipole) will flow between the shifting dendrites and the soma. This along with thalamocortical oscillations produces the EEG waves.The brain doesn’t churn out the rhythm just like that. Had the neurons fired randomly the oscillations would have cancelled out.EEG waves occur due to synchronous discharge of neurons producing the alpha, beta, theta, gamma and other telltale waves. Like all other electrical waves, they too have a frequency and amplitude. Alpha waves, for example, have a frequency of 8-12 Hz (cycles per second) and an amplitude ranging from 50-100 microvolt when recorded from the scalp, and it is found when a person is resting comfortably with eyes closed and the mind wandering. On the other hand, gamma rhythm has a frequency of 30-80 Hz, and it is found when a person is deeply engrossed on some work.It was known for a long time that the hippocampus exerted a role in learning by fostering long term potentiation (LTP) by aligning the neocortex, where memories are stored. The mechanisms behind this are now emerging. Sirota et al and Siapas et al have analyzed rat brains and found out that there were many localized gamma oscillators within the brain that gave rise to neocortical gamma bursts. These oscillators had varying frequencies but they phase aligned themselves with the arrival of hippocampal theta waves. A large fraction of pyramidal cells and interneurons too were phase aligned to the hippocampal theta rhythm.This is similar to a bar magnet aligning iron dust or other ferromagnetic materials by virtue of its magnetic field. Apart from the cerebral cortex, the cerebellar cortex and the hippocampus too can generate brain waves. Such a mechanism may explain the orchestration of many parts of the cortex (and hence the memory engrams they contain); and data synchronization and downloading to the hippocampus for memory retrieval. It also shows how hippocampus does the ‘indexing’ of cortical contents. These experiments throw light on neuronal plasticity and information flow, and may be someday they could help clinicians in fighting memory loss as it occurs in neurodegenerative diseases like Alzheimer’s disease.Last modified: neverReferences:Prefrontal Phase Locking to Hippocampal Theta OscillationsAthanassios G. Siapas, Evgueniy V. Lubenov and Matthew A. Wilson. doi:10.1016/j.neuron.2005.02.028A SIROTA, S MONTGOMERY, S FUJISAWA, Y ISOMURA, M ZUGARO, G BUZSAKI (2008). Entrainment of Neocortical Neurons and Gamma Oscillations by the Hippocampal Theta Rhythm Neuron, 60 (4), 683-697 DOI: 10.1016/j.neuron.2008.09.014... Read more »

A SIROTA, S MONTGOMERY, S FUJISAWA, Y ISOMURA, M ZUGARO, & G BUZSAKI. (2008) Entrainment of Neocortical Neurons and Gamma Oscillations by the Hippocampal Theta Rhythm. Neuron, 60(4), 683-697. DOI: 10.1016/j.neuron.2008.09.014

April 3, 2009
10:46 AM
868 views

An Anatomy of Noise And It's Implications

by Amiya in Physiology physics woven fine

Noise is something we dislike, because by definition, noise means unwanted sound. But this definition is subjective, for what is music to my ears (say the heavy metal band Metallica) is noise to most people. In fact Iraqi prisoners were forced to listen to Metallica songs as a means of torture (culture shock and noise) by the American soldiers. Perhaps a better definition is, wrong sound at the wrong place at the wrong time.Apart from acoustic noise; there is visual noise as found in television as ‘snow’, electronic noise (e.g. thermal noise or Johnson noise), cosmic noise and so on. Speaking of acoustic noise, one can’t help but think about the dreaded ‘noise pollution’ that seems to envelop us all. In addition to the nuisance it poses, it also causes anxiety, insomnia, increased blood pressure (hypertension), deafness and a hell lot of other bad things. So, it seems that noise is all bad. It’s not always so!There is a disease called otosclerosis. In this disease, the footplate of stapes (a small bone in the middle ear) gets fixed to the oval window of the internal ear, producing conductive deafness. The patient can not hear normally as the ossicular (bony) conducting chain is at fault. But surprisingly, such persons hear well in noisy places (market, railway station). This phenomenon called Paracusis Willisii is said to occur due to the fact that one has to speak out real loud (over and above the background noise) in such places; thus making this loud voice cross the patients’ threshold of hearing. However, it may also be possible that the amplitude of the voice (in decibel) might ‘ride’ (summate) on the background noise amplitude, and this combined sound amplitude is heard by the ears. The brain then does some kind of fuzzy logic (or acts as a differential amplifier); and the ‘information’ is decoded. So, it seems that noise isn’t all that bad.In ‘information theory’ even noise is said to contain information in it. One fine example that illustrates how visual noise might contain information is random dot stereography (and autostereogram). So, noise could be meaningful.In diabetes mellitus, a very common disease across the globe, the blood glucose level rises. This and other metabolic products causes a condition called diabetic neuropathy, among other things. The person’s sense of touch is diminished and this results in inattention to sustained pressure(causes decreased circulation) or trauma to the affected area. This, along with the increased blood glucose and infection may then cause gangrene of the limb which might require an amputation of that limb. Cloutier et al have resorted to noise in an attempt to address the issue.They applied mechanical noise directly over sensory neurons and have found that both vibration and tactile perception in these patients improved. This mechanical noise was christened as ‘stochastic resonance’ (stochastic means random or probabilistic; this particular term is coined since the frequencies are not tuned to match any particular frequency), and was applied at an imperceptible level. They applied this noise to the great toe of some of the affected individuals, while the controls received none (i.e. no SR). The effect was studied by measuring the vibration perception threshold (VPT). VPT was significantly lower in patients receiving SR compared to the controls (no SR). As the threshold was low, the patients’ sensitivity to detect vibration and tactile sensation improved. They hoped that a continually vibrating shoe insert could improve nerve function in these cases.In another instance, Toshio Mori and Shoichi Kai of the University of Kyushu, Japan, showed that noise might improve brain function. They shone periodic signals (of 5 Hz flicker) onto the right eyelids and noisy signals onto the left eyelids of the subjects when they were at rest, and measured the intensity of their brain waves. Brain waves are electrical signals that occur in the brain due to the firing of neurons and are detected by electroencephalography (EEG). They found a sharp peak at 5 Hz, the frequency of the periodic varying signal. As they increased the strength of the noise signal relative to the periodic signal, a ‘harmonic’ peak emerged in the alpha wave band at 10 Hz. As the noise signal gained strength, this peak first increased and then diminished. The researchers believe that this harmonic peak is indicative of stochastic resonance in the cerebral visual cortex. Stochastic because of the non-linear way the brainwave behaves in response to the external stimulus. They argue that naturally occurring background electrical noise in the brain (from electron transport chains, neuronal activities) may play important roles in cognition and behavior.However, not everything about noise is healthy as researchers from the University of California at San Francisco, USA suggest. They exposed healthy young rats to ‘white noise’, (random audio frequencies covering the full spectrum with randomly assigned amplitudes) and found that the development of their auditory cortex was delayed. They used electrophysiology tools to explore this. They also suspected that everyday environmental noise, also a type of white noise, could harm children by interfering with language acquisition and speech.The question is: should we scold our children when they continue with those awful noises? I am confused. But one more thing; it was this noise (in the microwave spectrum) that gave scientists the experimental proof that the Universe was expanding.Last modified: neverReference: Prolonged Mechanical Noise Restores Tactile Sense in Diabetic Neuropathic Patients.Cloutier R, Horr S, Niemi JB, D' Andrea S, Lima C, Harry JD, Veves A.Int J Low Extrem Wounds. 2009 Jan 6.Noisy signals strengthen human brainwavesT Mori and S Kai 2002 Phys. Rev. Lett. 88 218101White Noise Delays Auditory Organization in the BrainNoise, WikipediaMori, T., & Kai, S. (2002). Noise-Induced Entrainment and Stochastic Resonance in Human Brain Waves Physical Review Letters, 88 (21) DOI: 10.1103/PhysRevLett.88.218101... Read more »

Mori, T., & Kai, S. (2002) Noise-Induced Entrainment and Stochastic Resonance in Human Brain Waves. Physical Review Letters, 88(21). DOI: 10.1103/PhysRevLett.88.218101

January 28, 2009
01:34 PM
858 views

Period Concatenation in The Brain, And The Synthesis of Beta 1 Rhythm

by Amiya in Physiology physics woven fine

The principles of generation of EEG waves in the brain are still ill understood. Although the general mechanism of cortical dipoles and thalamocortical oscillations behind the generation holds true; there has been speculations that the alpha waves could actually be originating in the heart- the cardiac electromechanical hypothesis, which states that the arterial pulse ‘shocks’ the skull-brain mass (and interacts electrically and mechanically) to oscillate at its naturally resonant frequency of approximately 10 Hz.Now, Kramer et al propose that beta 1 rhythm could be the result of a process called period concatenation (concatenation means chain forming or serial addition). Beta rhythms (18-30 Hz) were thought to be harmonics (integer multiples of the fundamental frequency) of alpha rhythms (8-12 Hz). Kramer et al observed that application of 400 nanomolar kainate to rat somatosensory cortex produced gamma rhythm in the superficial cortical layers and beta2 rhythms in the deep cortical layers.They observed that after an initial interval of simultaneous gamma (~25 ms period) and beta2 (~40 ms period) rhythms in the superficial and deep cortical layers respectively, a resultant, synchronous beta1 (~65 ms period) rhythm in all cortical layers occurred. They concluded that the time period (the inverse of frequency, or 1/f) of gamma wave (25ms) concatenated with that of beta2 (40ms), to form the time period of 65 ms (40+25). That was the time period of the beta1 rhythm, which resulted as a consequence of this concatenation. They concluded that neural activity in the superficial and deep cortical layers of the brain could combine over time to generate a slower oscillation.Frequency synthesis would, naturally, have both energy and space saving implications for the system concerned. That the brain economizes is not new in computational biology and electronics. For example, in the simplest and realistic model of the 40 Hz gamma rhythm, only 2 neurons (one excitatory and the other inhibitory) interconnected by reciprocal paths are required. The excitatory neuron will ‘charge’ the inhibitory neuron. The inhibitory neuron will suppress (inhibit) the activity of the excitatory neuron as a result, and any oscillation will be dampened. Hence, a decay in the inhibitory synapse will not inhibit the excitatory neuron anymore and thus cause oscillation; and clearly, the frequency of rhythm will depend on the decay time. This “gamma-motif” resembles a lot with the ‘flip-flop’ circuits in digital electronics.Its not surprising that the human brain which had evolved as a result of nature’s selection process will learn to compute things so that the metabolic costs of additional neural pacemakers were curtailed to the bare minimum.Last modified: neverReferences: Mark A. Kramer, Anita K. Roopun, Lucy M. Carracedo, Roger D. Traub, Miles A. Whittington, Nancy J. Kopell (2008). Rhythm Generation through Period Concatenation in Rat Somatosensory Cortex PLoS Computational Biology, 4 (9) DOI: 10.1371/journal.pcbi.1000169A Cardiac Hypothesis for the Origin of EEG AlphaCastillo, Horace T. Digital Object Identifier: 10.1109/TBME.1983.325080... Read more »

Mark A. Kramer, Anita K. Roopun, Lucy M. Carracedo, Roger D. Traub, Miles A. Whittington, & Nancy J. Kopell. (2008) Rhythm Generation through Period Concatenation in Rat Somatosensory Cortex. PLoS Computational Biology, 4(9). DOI: 10.1371/journal.pcbi.1000169

October 19, 2008
05:21 AM
815 views

LTP Ensures That Memories Are Forever

by Amiya in Physiology physics woven fine

LTP or Long term potentiation is a process that may explain how memory gets stored in the brain for long term use. When you stimulate the presynaptic neuron by giving a brief (of transient duration) but rapid train of stimulus, the post synaptic neuron adjusts its ‘weight of association’ with respects to the presynaptic one, in the form of a chemical reaction. Though LTP occurs throughout the brain, it has been studied mostly in the hippocampus. If we are to understand the underlying molecular mechanism of memory, we can not do without LTP.Two different types of LTP are known: mossy fiber LTP and Schaffer collateral type LTP. While the basis of mossy fiber LTP is not clearly known; it involves modification of the presynaptic terminal, and is independent of NMDA. A schematic and functional diagram for Schaffer collateral LTP is presented here. But before that, allow me to digress a little bit.Your computer has a DRAM (Dynamic Random Access Memory) memory chip: memory because it can store and retrieve information, Random access as it allows you to search anywhere within the memory at random (it does not have to reach D via A-B-C, sequentially), and dynamic since the memory needs to be refreshed from time to time. To store a bit of memory, your computer charges ‘capacitors’ within the chip, which retain their charge, and read the memories stored as charges for later retrieval. But these capacitors lose their charge over time and hence dynamic refreshing is necessary to maintain their memory.You’ll now understand why this digital analogy as we discuss LTP. The picture on the left portrays a presynaptic neuron which discharges glutamate, the main excitatory neurotransmitter of the brain and the spinal cord. Glutamate after being released upon the stimulation of the presynaptic terminal, binds with their ‘receptors’ in the postsynaptic neuron. The post synaptic neuron, downstream, has 2 types of Glutamate receptors: NMDA (N methyl D Aspartate) and AMPA (alpha Amino 3 hydroxy 5 Methyl isoxazole 4 Propionate). Glutamate binds with both NMDA and AMPA receptors. NMDA receptors have a Magnesium ion, guarding at its channel entry. So, for NMDA receptors to act, it needs to be partially depolarized first, so that this magnesium block is removed. This is achieved by the AMPA receptors, which upon binding with glutamate, allows the entry of Sodium ions inside, thereby raising the cell voltage. NMDA receptors now swing into action as it now allows huge amounts of Calcium ions (and Sodium ions) to enter inside.These Ca then bind with Calmodulin present within the cell to form a complex, which then activates calcium-calmodulin kinase 2 (Ca/Cam k2). This newly formed compound then activates (phosphorylates) AMPA receptors, resulting in: 1) increased activity (conductance) of the already existing AMPA receptors in the cell membrane 2) Recruitment of AMPA receptors from within the cell to the cell membrane. So we can see that the synaptic strength is increased with each firing by both AMPA recruitment and increased AMPA conductance. The synapse stops at not only this, the postsynaptic neuron also discharges a ‘diffusible’ messenger, nitric oxide (NO), which 'tells' the presynaptic neuron to discharge more quantal release of glutamate next time. The phenomenon epitomizes Hebbian learning: Cells that fire together, wire together.But the memories so formed need to be stabilized as in the case of DRAM. In the central nervous system, dendritic spines are the main postsynaptic sites. These tiny protrusions form and change over a few hours. In hippocampal slice cultures it was shown, by De Roo and colleagues, that application of theta burst remodeled the dendritic spines; unused ones were shed (trimmed) while used ones were stabilized and new spines were formed. LTP was the chemical basis of all these modifications. They used GFP or green fluorescent protein for visualizing these changes of neural plasticity. However, they (physical units of memory) can also be seen by restorative deconvolution microscopy, in the form of flattened synapses (as if the ohmic resistance getting diminished in their electronic cousins) and hence more area for contact between the pre and postsynaptic neurons. So like DRAM chips, our memory chips too need to be constantly refreshed, even long term memories need maintenance.Mathias De Roo, Paul Klauser, Dominique Muller, Morgan Sheng (2008). LTP Promotes a Selective Long-Term Stabilization and Clustering of Dendritic Spines PLoS Biology, 6 (9) DOI: 10.1371/journal.pbio.0060219Last modified: neverReference: hyper-links, unless specifically mentioned... Read more »

Dominique Muller, Morgan Sheng, Mathias De Roo, Paul Klauser, & Morgan Sheng. (2008) LTP Promotes a Selective Long-Term Stabilization and Clustering of Dendritic Spines . PLoS Biology. info:/

March 20, 2009
01:11 AM
794 views

Peripheral Clocks Synch With The Master Zeitgeber

by Amiya in Physiology physics woven fine

In our bodies there are clocks in addition to the Master clock located in the suprachiasmatic nucleus. In computers, there are multiple clocks too, and they are tightly coordinated. For example, Integrated circuits like AV 9155 generate multiple clock frequencies for different portions of a computer (e.g. bus clock, CPU clock, keyboard clock etc.). All these clock frequencies are well regulated, since ICs like AV9155 use 2 quartz crystals (14.318 MHz) which generates of all these frequencies (they have inbuilt circuitry for dividing/multiplying these frequencies to create other necessary frequencies).Our bodies have their own version of these ‘crystal oscillators’, the BMAL1/CLOCK heterodimer. Since genes are present in all cells (leaving aside germ cells for a while, since they are haploid, and chiasma formation gives rise to gene rearrangement), theoretically all cells also has the machinery for BMAL/CLOCK generation. Thus in the periphery, where these genes are expressed, circadian oscillating mechanisms are automatically incorporated.The role of peripheral circadian clocks is still uncertain. But it is known that the peripheral clocks regulate cell division, estrous cycles and glucose and lipid homeostasis. Lamia et al knocked out the BMAL1 gene in mice liver and observed that the liver was no longer able to pour sufficient glucose into the blood circulation for cellular activity, resulting in hypoglycemia. Normally, the liver produces glucose from lipids and amino acids in a process called neoglucogenesis; and from glycogen, a glucose polymer, by glycogenolysis, in the fasting phase, to make up for the dwindling blood glucose level. In liver specific BMAL1 deletion, this did not happen and the animal suffered from hypoglycemia, indicating the important role of the liver peripheral clock.These peripheral clocks certainly need to be regulated too in order to achieve physiological harmony. The master clock in the suprachiasmatic nucleus might regulate these peripheral clocks by hormones and hemodynamic cues.Gatfield et al used two groups of mice and inactivated BMAL1 in all their cells in one group (BMAL1-/-); and only in liver cells in the other group (L-BMAL1-/-) [the 2 minus signs indicate homozygous, or in both alleles, deletion/inactivation]. The mice in which all BMAL1 were deleted did not show any problem which glucose homeostasis, whereas those with only liver specific BMAL1 deletion had problem maintaining normal sugar level in the inactivity (fasting) phase. Thus the role of liver clock is undeniable. The hepatic oscillator synchronises on feeding cues, since feeding is related to circadian metabolism. In the L-BMAL1 knockout mice, both neoglucogenesis and glycogenolysis operated adequately, but the machinery for the pouring of glucose into the circulation, the final step that is carried out by glucose transporter 2 (GLUT2) is suboptimal. GLUT2 expression in L-BMAL1-/- rats is inadequate.In BMAL1-/- mice, the master clock in the SCN was inactive along with all other peripheral clocks. This presumably abolished the circadian feeding responses and thus glucose homeostasis was minimally affected. It is as if both the SCN (master) and liver (slave) clocks gone wrong and they were fully asynchronous. But in the L-BMAL1 knockout mice, the SCN was OK and it expected the desired blood glucose level in the habitual feeding time, but the liver lacked GLUT2 to supply the required glucose in the bloodstream. UNITED WE STAND, we better synch!Last modified: neverReferences:Physiological significance of a peripheral tissue circadian clock. Katja A. Lamia, Kai-Florian Storch, and Charles J. Weitz doi:10.1073/pnas.0806717105BMAL1 and CLOCK, Two Essential Components of the Circadian Clock, Are Involved inGlucose Homeostasis. R. Daniel Rudic , Peter McNamara , Anne-Maria Curtis, Raymond C. Boston, Satchidananda Panda, John B. Hogenesch, Garret A. FitzGerald doi:10.1371/journal.pbio.0020377D. Gatfield, U. Schibler (2008). Circadian glucose homeostasis requires compensatory interference between brain and liver clocks Proceedings of the National Academy of Sciences, 105 (39), 14753-14754 DOI: 10.1073/pnas.0807861105... Read more »

D. Gatfield, & U. Schibler. (2008) Circadian glucose homeostasis requires compensatory interference between brain and liver clocks. Proceedings of the National Academy of Sciences, 105(39), 14753-14754. DOI: 10.1073/pnas.0807861105

April 5, 2009
04:07 PM
784 views

Capturing Thought, in Real Time

by Amiya in Physiology physics woven fine

Wouldn't it be nice if we mapped how the thought processes traveled across our brain, in real time? That's exactly what Mazahir Hasan et al of Max Planck Institute for Medical Research in Heidelberg, have enabled us to view, when an action potential (AP) is underway in the central nervous system (CNS). The researchers introduced fluorescent calcium indicator proteins (FCIP) into the brain cells of mice by means of viral gene vectors. Each time an AP was underway, a lot of ionic phenomena happened. For example, the fast Sodium channels (Na+) opened (letting positive charges to the interior of the cell) leading to depolarization, Potassium (K+) channels opened (to bring back the resting membrane potential to normal, since K+ egress out of the cells) and so on.Next , the impulse is transmitted to the post-synaptic neuron through the agency of neurotransmitters. But, for this 'coupling' between the presynaptic and postsynaptic neurons to occur; Calcium ion (Ca++) levels in the synaptic knobs of the presynaptic neurons must rise for effective degranulation of the presynaptic vesicles. And that's precisely these researchers were banking upon.Just before the degranulation of synaptic vesicles begins; calcium ion concentration surges. Such short calcium currents peak within milliseconds, making them the appropriate ions for studying fast neuronal activity. Previously scientists had measured such currents by using microelectrodes implanted within the brain; but this method was quite unsuitable in studying moving animals or for a longer time period. So, they went on to produce stable transgenic mouse lines responding to functional calcium indicators; (including 'inverse pericam' and 'camgaroo-2') using viral vectors. These transgenic mouse lines were under TET inducible promoter (tetracycline, a broad-spectrum antibiotic) control. The TET system offered the advantage of targeting combination of different neuronal cell assemblies. The other side of the Ptetbi (bidirectional promoter tetracycline) promoter was attached to the firefly luciferase gene. They were also sensitive to doxicline (another antibiotic belonging to the same category as tetracycline) in terms of regulation of luciferase, as well.They then used a heteromeric sensor protein called D3cpv, which was made to produce in the nerve cells of the transgenic mice. Two subunits of this protein reacted to the binding of calcium ions in a way that when the yellow-fluorescent protein (YFP) lit up and the cyan-fluorescent protein (CFP) intensity diminished. When calcium was bound to the D3cpv complex; CFP (cyan fluorescent protein) and YFP (yellow fluorescent protein) came closer together bringing about FRET, in such a way that there was a visible color change, 'visually' or optically indicating the progression of action potential in real time. CFP and YFP are spectral variants of GFP linked together by a Ca++ sensitive linker.They used 'two-photon imaging microscopy' to study this phenomenon. They excited thinned out rat skulls using two-photons simultaneously using 'mode-locked' Titanium-sapphire laser. They then amplified the signal using photomultipliers and analyzed them.The resolution of the experiment was limited to less than 1 Hz (frequency of action potentials). They conferred that human thought processes might be mapped in much the same 'opto-physiologic way', in contrast to the usual electrophysiologic approach. Not only does the experiment throw light on the thought processes in real-time, but also, it is expected that it will be useful in the pathophysiology and treatment of Alzheimer's disease, Parkinson's disease and Huntington's chorea.FCIP-positive cells were found in the hippocampal CA1 and CA3 regions, mossy fiber areas of the dentate gyrus, neocortical pyramidal cells and olfactory receptor neurons, they remarked. They studied cortical pyramidal cell, olfactory and optical responses in the mice in their experiment.Hasan, M., Friedrich, R., Euler, T., Larkum, M., Giese, G., Both, M., Duebel, J., Waters, J., Bujard, H., Griesbeck, O., Tsien, R., Nagai, T., Miyawaki, A., & Denk, W. (2004). Functional Fluorescent Ca2+ Indicator Proteins in Transgenic Mice under TET Control PLoS Biology, 2 (6) DOI: 10.1371/journal.pbio.0020163Last modified: neverReference: Damian J Wallace, Stephan Meyer zum Alten Borgloh, Simone Astori, Ying Yang, Melanie Bausen, Sebastian Kügler, Amy E Palmer, Roger Y Tsien, Rolf Sprengel, Jason N D Kerr, Winfried Denk & Mazahir T Hasan. doi:10.1038/nmeth.1242... Read more »

Hasan, M., Friedrich, R., Euler, T., Larkum, M., Giese, G., Both, M., Duebel, J., Waters, J., Bujard, H., Griesbeck, O.... (2004) Functional Fluorescent Ca2 Indicator Proteins in Transgenic Mice under TET Control. PLoS Biology, 2(6). DOI: 10.1371/journal.pbio.0020163

March 20, 2009
01:11 AM
767 views

Peripheral Clocks Synch With The Master Zeitgeber

by Amiya in Physiology physics woven fine

In our bodies there are clocks in addition to the Master clock located in the suprachiasmatic nucleus. In computers, there are multiple clocks too, and they are tightly coordinated. For example,...

[[ This is a content summary only. Visit my website for full links, other content, and more! ]]... Read more »

D. Gatfield, & U. Schibler. (2008) Circadian glucose homeostasis requires compensatory interference between brain and liver clocks. Proceedings of the National Academy of Sciences, 105(39), 14753-14754. DOI: 10.1073/pnas.0807861105

March 20, 2009
12:59 AM
743 views

Quantum Biology: The Spooky NanoWorld of Molecules

by Amiya in Physiology physics woven fine

We are quite adept in solving numerical problems in our everyday ‘analog world’ using decimal rules developed by us. Digital computers, on the other hand, calculate using binary or Boolean (0, 1) rules, and then convert the result in decimal format with the help of dedicated binary to decimal converter ICs. In the molecular world, calculations ‘happen’ in a strange way.Take for example the case of Fluorescent Resonant Energy Transfer or FRET. Also known as Forster Resonant Energy Transfer, this phenomenon is characterized by the emission of a photon of one frequency (upon stimulation) which, in turn, activates an acceptor molecule to emit a photon of another wavelength. There’s one clause that says that the first photon (from the donor molecule) will only be emitted when it can definitively be coupled with the ‘acceptor’. But in the first place, how is this ‘virtual photon’ to know whether its bride was waiting or not when it hasn’t even visited her? Yet FRET doesn’t fret, and the process goes on.All plants use chlorophyll to trap sunlight and convert it to chemical energy in the form of carbohydrates by photosynthesis. The efficiency approximates 100%. The predominant classical approach was that the photons hopped from light capturing pigment biomolecules to the ultimate reaction center where the actual conversion was taking place. But this ‘first choose and then pick’ approach that classical physics suggested would mean considerable loss of energy as heat, as photons wasted time as they hopped down the energy ladder. Quantum mechanics bypassed this by allowing simultaneous sampling of all energy states at one go by its unique properties of ‘superposition’ and ‘entanglement’. Graham Fleming and researchers at Lawrence Berkeley National Laboratory and the University of California at Berkeley showed the existence of a process of ‘quantum beating’, (a phenomenon akin to 'heterodyning’ in radio sets that is used to obtain intermediate frequencies for amplification) occurred which allowed sampling of all energy states by interference of the propagating wave. They used two-dimensional electronic spectroscopy in order to probe the sequence of events that occurred.That the RBCs (erythrocytes), actomyosin complexes use quantum mechanics for system optimization has been established. Cellular respiration in the mitochondria, DNA, and the brain too might exploit quantum computing.Counting without disturbing the molecule may be achieved by quantum mechanics, for it allows a molecule to know as if ‘intuitively’, the state of another molecule placed at a distance. Erwin Schrödinger, in his book 'What is Life?', opined that biological systems could be using the principles of quantum theory to maintain biological order. Sir Roger Penrose along with Stuart Hamerhoff proposed that the brain could be working as a quantum computer. In reaction to this, Max Tegmark showed that environmentally induced decoherence would foil any quantum interaction taking place. But Tegmark assumed the average kinetic energy (temperature) of the brain as 310 K (273+37). While this is true in a macroscopic world, Koichiro Matsuno has shown, using black body radiation measurements, that actomyosin complexes which are abundant in the axons of nerve cells, can reach local temperatures as low as 1.6*10-3K. It is as if nature has evolved ways to ensure decoherence free subspaces where entanglement and quantum interaction were possible. Stephen Hawking in his book 'A Brief History of Time' observed that quantum mechanics was the basis of modern biology and chemistry and the only area where quantum mechanics was not properly integrated were gravity and the large-scale structure of the universe (page 60).To quote Ogryzko "Indeed, if it has taken Humankind only few decades to approach the use of entanglement in quantum information technology, one can wonder why Life, in billions of years of evolution, could not also learn to take advantage, finding in entanglement an alternative resource for stabilizing biological order." It seems we need an entirely different approach if we wanted to probe the mysteries of life and quantum theory is poised to help us in this regard.Last modified: neverReferences:Quantum BiologyVasily V Ogryzko (2008). Erwin Schroedinger, Francis Crick and epigenetic stability Biology Direct, 3 (1) DOI: 10.1186/1745-6150-3-15... Read more »

Vasily V Ogryzko. (2008) Erwin Schroedinger, Francis Crick and epigenetic stability. Biology Direct, 3(1), 15. DOI: 10.1186/1745-6150-3-15

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