Author Amit Kulshrestha & Dhanya Nair, Feb 18, 2006

Synopsis : This article and illustrations seek to explain the application of Proteomics and Genomics to combating the H5N1, avian influenza virus. A brief description of both fields precedes an explanation of gene expression. H5N1 protein structure clarifies which protein causes infection and then the applications of latest technologies combating H5N1 are detailed.

Genomics : Genomics studies the entire DNA sequence of an organism's genome and the use of the genes. It refers to the study of all of the nucleotide sequences, including structural genes, regulatory sequences, and non-coding DNA segments, in the chromosomes of an organism. The goal is to find all the genes within each genome, find what genes do, how they are controlled, and how they work together.
It looks at all the genes as a dynamic system, over time, to determine how they interact and their physiology, in global manner.

It uses this information to understand molecular mechanisms of disease, answer scientific questions and to develop improved medicines.

Proteomics :
Proteomics is the study of structures and functions of proteins. It is different from and more complex than genomics. It can be understood as proteins expressed by a genome.

Proteomics includes the identification, abundance, spatial distribution and quantification of proteins, but also determines their localization, modifications, interactions, activities, and their function. With the sequencing of genomes of many biological organisms, the scope of Proteomics has broadened from protein identification and characterization to analyzing the protein structure, function and protein-protein interactions.

Identifying proteins: To identify proteins, x-ray crystallography; nuclear magnetic resonance (NMR) spectroscopy are being used. Protein arrays are also being used; they consist of a library of hundreds or even thousands of different proteins spotted individually in a known location on a chip. It uses the proteins themselves for studying the protein/ protein interactions or of probes (often antibodies) for capturing proteins.
Protein arrays are more difficult to work with than DNA arrays as proteins vary hugely in their chemical nature. They also bind to each other in several ways. In contrast, DNA fragments, only the nucleotide sequence varies and they pair by simple Watson-Crick base method.

Problem in Proteomics and Genomics: Proteomics can overlook proteins that are present in minute quantities, and genomics does not indicate the extent to which transcripts are translated into proteins. Companies are now producing plasma Immunodepletion Kit, that removes about 99% of twenty high abundant plasma proteins, thereby making it easier to visualize low-abundance proteins in samples.

Comparison between Proteomics and Genomics :

Proteomics	Genomics
Refers to all the proteins produced by an organism	Refers to the entire set of genes in an organism (haploid set)
Proteins are responsible for both the structure and the functions of all living things, life is due to proteins. Usage: Catalyze enzymes As messengers- neurotransmitters Regulate cell reproduction Defensive action (antibodies) Tissue growth Oxygens transport	Genes are the instructions for making proteins (Genes-mRNA-Proteins).
Proteome varies from one cell type to another in an organism although all have the same genome. It varies in RBC to WBC to neuron, fibroblast, It also varies with health or disease and also with time for a cell during its lifecycle as it responds to environment i.e. new nutrients, hormones, foreign bodies etc.	Genome remains unchanged from one cell to another (except for mutations or un-repaired damage to its DNA)
Complex: A single gene can give rise to a number of different proteins due to formation of glycoproteins, addition of phosphates to amino acids, RNA editing	Relatively simple and constant
Humans : 400,000 proteins (each having different functions) made by genes	Humans : 22-23000 genes Virus : 3- 200 genes

Gene to proteins:

A gene is a section of genome that carries information for the construction of a protein.

A protein is constructed by joining a sequence of amino acids. The precise amino acid content, and the sequence of those amino acids, of a specific protein, is determined by the sequence of the bases in the gene that encodes that protein. Thus in short the sequence of amino acids present in a protein is compiled corresponding to the sequence of bases of a gene.

The path leading from genes to proteins involves two steps called transcription and translation.

Transcription takes place in the nucleus of the cell. In this step, the gene of the genome molecule is copied to a strand of RNA molecule called Messenger RNA (mRNA).Thus translation is the process of converting the mRNA codon sequences into an amino acid sequence.

Translation is the step that finally converts the copied code of mRNA to proteins. The process of protein synthesis takes place at the site of ribosomes that are present in the cytoplasm of the cell.

In this process mRNA leaves the nucleus, travels to the site of ribosomes. Here at this site as per the code, amino acids are collected and linked together to form the appropriate protein molecule.

Ribosomal RNA and Transfer RNA assist the process of translation.
Messenger RNA (mRNA) is used for construction of a protein.
Ribosomal RNA (rRNA) is the construction site where the protein is made. Transfer RNA (tRNA) is the truck delivering the proper amino acid to the site at the right time.

Amino acids link up in a chain format to form large molecules called proteins. There are 20 different amino acids. They combine in different combinations to form thousands of proteins. The order of amino acids in the protein molecule determines its structure and function. The final protein molecule may consist of several hundred amino acids linked together according to the instructions encoded in the mRNA. In addition, each protein can undergo a variety of post-translational modifications that further influence its shape and functions. Proteins may serve e.g., as enzymes, hormones or structural components of a cell.

H5N1 (bird flu virus) & its proteins:

The H5N1 infects a human or bird using its proteins on its envelope, inhibiting its proteins could curtail the infection from occurring or spreading.

However in the replication process mutations or recombination occurs, altering its genome sequence sufficiently enough to create a new set of proteins, for example the H5N1 virus can now infected the ciliated cells of bird, humans and pigs though structurally they are different.

Lets look at its major proteins, some of them have been described below, and refer the animation for more details.

Haemagglutinin (H or HA): These spike like projections present on the envelope, help the virus recognize and attach itself to the cells of the host. .They are made up of carbohydrate & protein complexes. Haemagglutinin is a 135Å trimer, that binds to mucoproteins (found on the surface of epithelial cells) containing terminal N-acetyl neuraminic acid. This protein is also responsible for membrane fusion in virus entry.

N : Neuraminidase (N or NA ): These spike like projections, made up of carbohydrate & protein complexes, present on the envelope allows newly formed virus particles to break free from their host cells. It is crucial to this budding and release process. It is a 60Å tetramer. The nucleic acid in A and B types are arranged in 8 segments (7 for influenza type C). Each segment comprises of single strand, negative sense RNA2 associated with three polymerase polypeptides giving RNP.

Ion channel M2 : pH activated ion channels (M2) are involved in the uncoating process of the virus.

M1 ( Matrix protein) : In the virus particle, the vRNPs are connected to each other and with the viral envelope by the matrix protein,

NS1: Anti-interferon protein. Effects on cellular RNA transport

Using Proteomics/Genomics to fight H5N1

The problem is that every time an animal is infected, H5N1 virus gets an opportunity to mutate its genetic code. It is in a process of rapid evolution, at present four variants of it are in circulation.

Drug development (Oseltamivir or Tamiflu): Identification of the structure of viral protein helps in creating the drugs. The drug Oseltamivir works by decreasing the ability of influenza virus to spread from infected cells to uninfected cells by inhibiting neuraminidase, the protein required for the virus to exit infected cells.

However a recent study has shown that Oseltamivir has to be used for eight days in mice to suppress the virus, the virus continues to grow if the drug is stopped after five days.

By identification of NS1 Protein: In Jan 26, 2006, scientists were able to identify through prototyping, a wide analysis of the genome sequences of different virus strains (avian, swine, and human influenza sequencing data), a unique protein responsible for the high mortality of H5N1. The protein NS1 (having a bird origin) works in combination with other avian flu proteins, within the infected cells and disrupts key cellular processes in humans.

Viruses in which the entire complements of influenza genes, including NS, were derived from an avian source caused the recent H5, H7 and H9 outbreaks in Asia. Thus the introduction of avian NS1 into human cells can potentially disrupt many cell pathways...while the human NS1 does not.

The protein NS1 might become a key target for future anti-flu drugs.

By CombiMatrix DNA arrays (using genomics): CombiMatrix group has made commercially available the first microarray designed for the H5N1 "Bird Flu" influenza A virus. The conventional approach to materials discovery involved successive cycles of synthesis and testing, making the process costly, labor and time intensive. The new approach is speedier and more economical as it enables the synthesis of many thousands of materials in parallel followed by testing of all of those materials at one go.

CombiMatrix's DNA microarray employs the parallel synthesis of large numbers of nano-structured materials. These materials are tested using the chip-based technology. It not only allows for the identification of the H5N1 virus but also the tracking of mutations as the virus moves from host to host. The chip measures about 22 mm by 5 mm. Below it is one of the thousands of microelectrodes per chip where DNA is synthesized and controlled by the digital circuitry. The arrays of oligonucleotides capture molecules synthesized on the chip for use in Genomic and Proteomic applications.

By PCR based test (using genomics) : Roche Diagnostics and Tib Molbiol, Berlin, Germany, announced the worldwide availability of a new PCR-based test designed to allow researchers detect the influenza A virus H5N1 in birds.

It uses a technology platform that is commonly available in research laboratories. It allows for identification of the Influenza A H5N1 subtype within hours compared to days with many other methods. The test also detects genetic material of the virus instead of proteins (antibodies) that are identified by other immunological tests currently used.

By Direct RNAi™ (using both) : Alnylam Pharmaceuticals and University of Georgia jointly will work to discover short interfering RNAs (siRNAs) to target key flu genes required for virus replication.

The process of DNA -- RNA - protein at times produces abnormal proteins causing human disease. RNAi inhibits the production of abnormal proteins by gene silencing (through silencing mRNAs).

Many of the best-selling drugs today either act by targeting proteins or are proteins themselves. Advances in proteomics are helping scientists create medications that are "customized", more effective and have fewer side effects.

Author Amit Kulshreshtha

Nerve cells require oxygen and glucose to transmit impulse, in this article I will discuss what is the role of each constituent into propagation of impulse. A look at the structure and composition of neuron and neuronal transmission mechanism will help in understanding the concept.

What are neurons?
The nervous system in the human body is made up of billions of nerve cells, or neurons, organized in various networks. The majority of these neurons are located in the brain, brain stem and spinal cord comprising the central nervous system (CNS).

Each nerve cell or neuron has a central portion containing the nucleus ( cell body) and one or more extensions protruding from the cell body called axons and dendrites.

• A cell membrane surrounds neurons.
  
• Neurons have a nucleus that contains genes.
  
• They also contain cytoplasm, mitochondria and other "organelles".
  
• They carry out basic cellular processes such as protein synthesis and energy production.
  
• They have specialized extensions called dendrites and axons. Dendrites bring information to the cell body and axons take information away from the cell body.
  
• Neurons communicate with each other through an electrochemical process.
  
• They contain some specialized structures like synapses and chemicals like neurotransmitters
  
• Dendrites receive nerve impulses from other neurons or from sensory receptors.
  
• The axon carries the nerve impulses (action potential) away from the cell body to another neuron or to a muscle. Axons can be very long-up to a meter in the case of a neuron that reaches from the big toe to the base of the spinal cord.

Neurons need energy to function :
Like all the other cells in the human body, neurons need energy to function. They consume an especially large amount of energy. The brain is only 2% of the human body's weight, but consumes about 20% of energy. Its consumption is about 25 watts.

Neurons consume oxygen and glucose for fuel. The more challenging the brain's task is, the more fuel it consumes. This energy is produced in the mitochondria. There are hundreds or thousands of mitochondria in neurons. They use oxygen to extract energy from glucose and fats and to produce molecules of the energy-storage compound adenosine triphosphate (ATP). These ATP molecules are then used to fuel the various chemical reactions that take place within the neuron.

Proof of energy consumption : Using fMRI (functional Magnetic Resonance Imaging), it can be detected that active neurons consume oxygen . The blood supply of the brain is regulated to give active neural assemblies more energy whilst inactive assemblies receive less energy. This dynamic regulation of the blood flow (called haemodynamic) is the principal on which fMRI is based.
When neurons fire, they consume oxygen. Nearby capillaries dilate in response to the oxygen deficit, thereby infusing the region with oxygen rich blood. This slightly increases the proportion of hemoglobin that has been stripped of oxygen relative to the amount of hemoglobin carrying oxygen. The magnetic properties of hemoglobin-molecules in red blood cells that transport oxygen to the brain-differ when they are carrying oxygen. Optically hemoglobin without oxygen reflects less red light than hemoglobin with oxygen, active areas look slightly darker.
Thus neuronal activity affects the ratio of oxygenated and deoxygenated hemoglobin in the brain.
FMRI can track this increase in blood flow and generate increasingly intense images of heightened brain function. This implies that activated neurons do increase their consumption of oxygen.

Neuronal Transmission - The impulse needs energy :
Neurones send message electrochemically. Neural transmission relies on the rapid and precise delivery of chemical signals along neurons and across the spaces between them.

When a neuron is not sending a signal, it is at 'rest'. Its membrane is responsible for the different events that occur in a neuron. A strong stimulus like touch, pressure, stretching, sound waves, motion to the dendrite of a neuron initiates a nerve impulse. The impulse begins as an exchange of ions across a localized area of the plasma membrane.

The stimulus makes the nerve cell secrete a hormone, changing the permeability of outer cell membrane of the axon to positive ions that allow electrically-charged ions to move in and out of the cell . The influx of positive ions reduces the electrical potential across one segment of the membrane (depolarization). This reversal of polarity causes the same change in the neighboring area of the membrane, which causes a reversal of polarity further along, and so on. This impulse travels along the axon as a self-generating chain reaction. This is what really occurs when a nerve is described as "firing." Nerves do not conduct electricity or any other form of energy.

The impulse propagates along the length of the neuron as a cascade of ionic exchanges. It does not lose energy as it travels because it is continually regenerated at each new site along the membrane. Maintaining these ionic gradients is an energy-consuming process that requires a constant supply of glucose and oxygen to the neuron. Lack of glucose and oxygen deplete the cellular energy stores required to maintain electrical potentials and ion gradients. The energy of a nerve Impulse has been calculated to be 5 x 10-15 joules on an average, it may vary because of nature of sheath. As the supply of oxygen decreases the energy of the impulse also decreases. Lack of glucose and oxygen deplete the cellular energy stores required to maintain electrical potentials and ion gradients. The oxygen or energy requirement can be judged from an experiment performed at University of Rochester

The resting rate of oxygen consumption of the excised sciatic nerve of the frog is 1.23 c.mm. of oxygen per gm. of nerve per minute during stimulation with an induction coil with 100 make and 100 break shocks per second there was an excess oxygen consumption amounting on the average to 0.32 c.mm. of oxygen per gm. of nerve per minute of stimulation, or a 26 per cent increase over the resting rate thus establishing the importance of energy in neuronal transmission.(source :www.jgp.org/cgi/content/abstract/10/5/767)

For understanding more about neuronal transmission, view our animation, click here

By Amit Kulshreshtha
Bird flu virus : Bird flu virus has been in the news quite lately and lot of coverage has been allocated to it in newspapers and TV channels, but few know that this is the third biggest wave of virus infection, this wave started in 1997 and has been on a killing continuance, it has killed 120 million birds till date This is not just a figure, in Asia this would mean the owner of poultry farms face sudden poverty and distress that does not last for days but for months, as people shun eating chicken. In last scare, about two years ago, in India about $400 million losses were thrust on the poultry and egg sellers and for a developing country it was a nightmarish burden.

Bird Flu the virus is nothing but influenza viruses on a killing spree, actually some influenza virus in milder form give us runny nose and cough regularly. People also die due to complications resulting from it like pneumonia all over the world on a regular basis, so what is so special about this "bird flu virus" that is sending the alarm bells ringing all over the world, so much so that if you feed in "bird flu " in google you will get 45,200,000 pages for it.

Why is there a confusion about this virus ?
There have been two ways of getting confused about any concept
1) Inadequate knowledge available
2) Plethora of knowledge available
Sadly this has been the case with bird
People are selling herbal solutions, masks, T-shirts also in the name of bird flu. There are website explaining it spread and the unavoidable pandemic, but none is "showing" in exact detail what to do about it. So we did that.
Evolution of the killer : The virus has been slowly and steadily evolving keeping in step with process of evolution that every species undergoes. As various strains mix together in the backyard poultry, wild birds and pigs, a new strain comes into being. There is practically no vaccine for us against H5N1, and right now it is our good luck that is saving us from a pandemic, because present strain of H5N1 is only 0.18% different from big killer of 1918 that killed 40 million people. It has a 100% kill rate in birds and 60% of humans infected till today have died. So this is definitely a killer virus.

Antivirals : There is a big noise about antivirals being able to cure and save us from influenza, the problem is that it is difficult to differentiate between avian influenza and other viral infections, the symptoms need to identified well within 48 hours of infection,for the antiviral to be effective, it is not a easy task, even after a dose is taken the process of infection gets slowed down but is not eradicated. It may still kill its victim. The worst scenario will be when virus develops an immunity to the antivirals as it has done in case of amantidine. Survive it :It is a juggernaut and very few that have been infected by it have survived it . The best way to survive this virus is to avoid it, but avoidance needs understanding it first, it is invisible to begin with, so we need to identify its sources and transmission mechanism , we need to know what it is and how it infects us and our pets and poultry. We, at Goalfinder have endeavored to research out this virus in order to find answers for ourselves what we have found is shown through our movies , the films that we have developed are a result of our efforts towards presenting "correct information", in a simple and entertaining manner. The films have received wide appreciation.

We have put on site 5 movies on bird flu. These are animated comic book style simple explanations for bird flu for so many of those around who are confused about it. Also there is a bird flu map that can be downloaded for free, it tracks the instances of bird flu around the globe.

These are worlds' only movies explaining bird flu. Together they will answer 160 questions on bird flu.

They are
1) Surviving bird flu movie - This movie shows you the methods by which you can protect yourself from bird flu
2) Protecting pet birds and poultry from bird flu - This movie shows the method by which you can protect them from bird flu
3) Bird Flu - the virus - Part1
4) Bird Flu - the virus - Part2
5) Bird Flu - Seminar movie
6) Bird Flu - Tracker (map)

This is the advanced version of surviving bird flu, this intensive animated movie answers questions like how can a bird virus infect humans? What is a virus? And why vaccines don't work against it?
Now to answer the question what was the need to create movies on bird flu ? I believe that "seeing" is better than just "reading". "Seeing" a story unfold in front of us conveys a better meaning that just reading it.

We have answered questions like
What is a virus?
How does it function?
How can bird flu virus can be survived?
Howcan it be destroyed ? And many more questions.. in our animation.

There are more than 160 questions answered, Just go to the respective pages.

This File containing details of all three movies will give you a detailed look in the product, please give us a feedback so that we can improve the product

In LPAI, in poultry, mostly clinical signs are absent, indications are mild respiratory disease, depression, and decrease in egg production;

Clinical signs for HPAI are: depression, excessive thirst, open mouth breathing, loss of appetite, decreased egg production, nervousness, swelling or blue discoloration of combs and wattles, edema around eyes, coughing, star gazing, sneezing, rales and excessive lacrimation. Sudden death can also occur.

Watch this flash animation on clinical symptoms of bird flu.

 

View this flash animation in Full Screen ( pop ups should be allowed)

Our other movies and posters on bird flu - Click on the image

Virus movie
Bird Flu Virus Part 1
Bird Flu Virus Part 1
Bird Flu Virus in poultry
Poster on bird flu virus
poster on bird flu virus

What is interesting about water?
Water has curious thermal properties. It contracts (gets denser) as it cools down just like other materials. However, at 4 degrees Celsius, it reaches the maximum density of 1 and then starts expanding if it is further cooled. Ice formed at zero deg Celsius is actually less dense than water and floats on it.

Is the structure of liquid water same as that of ice?
No, ice is crystalline and with an ordered structure. This is less dense (has more space) than liquid water where even though H2O molecules are closely packed together but are still free to move around.

What is the structure of a water molecule? How does hydrogen bond form?
The atoms in the water molecule have the two H-O bonds at an angle of about 104.5° rather than directly opposite sides (180^o) of the oxygen atom. The molecule has non-linear bent shape closely resembling a boomerang (kind of letter ’V’).
A water molecule is polar in nature; Oxygen atom is highly electronegative and there is a net negative charge toward the oxygen end (the vertex) of the V-shaped molecule and a net positive charge at the hydrogen end. This electric dipole attracts the opposite ends of neighboring water molecules, where each oxygen atom attracts two nearby hydrogen atoms of two other water molecules. This attraction results in formation of a weak bond called ‘Hydrogen bond’. This forms between O-H pair of different water molecules.

Electronegative Oxygen is more negative than hydrogen, the molecule has a 'V' shape and is polar in nature, a hydrogen bond forms between two molecules

More details about hydrogen bond:
Hydrogen bonding has been observed in hydrogen compounds. Water is a liquid at room temperature because of it. Molecular weight of water is lesser than that of oxygen, carbon dioxide etc. at room temperature, however it is still liquid instead of a gas. This is due to the hydrogen bond that considerably weaker than the covalent bonds holding the water molecule together, but strong enough to keep water liquid at ordinary temperatures. In liquid water, as molecules slide past each other, bonds form, break, and re-form, iIt keeps the water molecules loosely bound to each other even when they are moving and keeps them together otherwise they would move far away from each other.

How does the hydrogen bond make the water expand as it cools?

 
(To view a bigger image click here)
Below 4 deg C water forms stable bonds and when frozen forms a rigid lattice with long bonds and space

Upto 4 degree Celsius : As water-cools from room temperature to 4 degrees Celsius, it becomes denser, as most liquids, the molecules have less kinetic energy and are closer together. The positive ends of some water molecules attract the negative ends of other water molecules and hydrogen bonds form.  When water reaches 4 degrees Celsius, the molecules have been pushed as closest to one another and the density of water becomes 1.00. water expands only by 0.01% as it cools from 4° to 0° Celsius but it will expand to 8.7% as it freezes.

Below 4 degree Celsius (277 K) : Below 4 degrees, each H₂O molecule begins to form more stable hydrogen bonds, with up to four fellow molecules. At zero degrees Celsius, the H2O molecules are lined up in a rigid frozen crystal lattice, an open hexagonal (six-sided) structure of ice.  This requires the water molecule to widen the angle between the O-H single bonds from the usual 104.5 degrees. Water expands about 8.7% when it freezes at a temperature of 0° Celsius

In the crystal structure of ice, each O-atom is surrounded tetrahedrally by four H-atoms. Two H-atoms are linked with O-atom by covalent bonds and the remaining two H-atoms are linked to O-atom by two H-bonds. Thus in ice every H₂O molecule is associated with four other water molecules by H-bonding in a less dense tetrahedral fashion. This gives rise to an open cage-like tetrahedral structure of ice with a large empty space due to the existence of H-bonds (see graphic).

When ice melts, some of the H-bonds in the cage-like structure are broken & the space between water molecules decreases i.e. water molecules come closer to each other. It implies that the water molecules lie closer to each other in the liquid state than in the solid state.

What are the effects of anomalous expansion of water?
In a lake or sea, as water is cooled from, higher temperature to 4 deg Celsius it becomes denser and sinks to the bottom but as it cools from 4 to freezing point, its density reduces as it expands and it rises to the top and eventually forms ice. The floating ice acts as insulation preventing the freezing of water below it, ensuring that life survives. If ice were heavier than water, it would sink to the bottom eventually whole of the lake would freeze, destroying any life in it. If the summer heat is unable to melt it, it would remain frozen, and without water, and the resulting rains, life on parched land will eventually die.

Fishes and aquatic life survives due to anomalous nature of water, ice being lighter than water floats and insulates the water below it from freezing.

Author - Ms. Dhanya Nair

Note : Also check out the higly detailed animation on our site
Discovery of electron by JJ Thomson
Discovery of Nucleus by Rutherford
Millikan's Oil drop experiment

The discovery of electron by J.J Thomson demonstrated for the first time that atoms were further divisible into tiny parts.

During the same period Curies studied an interesting phenomenon called radioactivity and found that some heavy elements like Uranium, Radium etc. are capable of emitting radiationconsisting of charged particles. This phenomenon gave substantial evidence that atoms were made up of tiny positively and negatively charged particles.

Lord Rutherford later on while studying the nature of these radiation discovered that the radioactive elements emit three types of radiations with different penetrating power namely alpha (least penetrated), beta (moderately penetrating) and Gamma (highly penetrating). When these radiations were subjected to electric fields, alpha rays were found to be positively charged particles while beta rays were found as negatively charged light particles. Gamma rays were found to be neutral in nature.

While studying the properties of these radiations, Rutherford noticed that the beam of alpha rays when were made to fall on a photographic plate by passing it through air, the edges of the slit became diffused and widened. He concluded that the alpha rays were scattered by air molecules.

To get a clearer evidence about the scattering he along with his coworkers Geiger and Marsden built an apparatus to bombard alpha particles on thin metallic foils. The metallic foil he selected for his experiment was a very thin gold foil.

Rutherford expected the atoms to be as suggested by Thomson. According to Thomson's model, atom is a ball of uniformly distributed positive charge with electrons embedded inside the sphere. This model is called as Plum pudding or chocolate chip cookie model.

Now if the atoms were actually arranged according to Thomson, then the alpha particles would go undeflected. (Since the electrons are too tiny to deflect the massive alpha particles while the deflection caused due to repulsive force acting between the positively charged particles and the alpha particles is very less).

But during experimentation it was found that though most of the alpha particles went right through the thin foil, a few alpha particles rebounded almost directly backwards. These large angle deflections were not consistent with Thomson's model.

From the above observations he concluded that large scattering angles
could only occur if most of the mass of the atom, and all of its positive charge reside in a very small, extremely dense region called the atomic nucleus. Most of the total volume of the atom is empty space in which electrons move around the nucleus.

On the basis of these postulates he was able to explain the -scattering experiment, most particles pass directly through the foil because they do not encounter the minute nucleus; they merely pass through the empty space of the atom. Occasionally a particle comes into the close vicinity of a gold nucleus, however. The repulsion between the highly charged gold nucleus and the particle is strong enough to deflect the less massive particle.

Thus Rutherford established a new model of the atom that was similar to the structure of planets in orbit around the sun. Rutherford's model consisted of a dense positive core at the center of the atom with electrons orbiting around it. This is called as Planetary Model of the atom.

Though Rutherford was successful enough to explain the rearrangement of the charged particles within the atom, his model faced some serious problems.

Problems faced by Rutherford's Atomic model:
If the model was correct, then one could show that atoms should not exist for more than a fraction of a second. However atoms were always found to be present from time immemorial i.e. Rutherford's atom was found to be unstable.

Rutherford's atomic model was unstable:

According to Rutherford's atomic model the electrons revolve around the nucleus in circular orbits. Now an orbiting electron is accelerated due to the centripetal force acting on it. Any accelerated charge particle loses its energy by emitting electromagnetic radiation.

This radiated energy would be at the expense of the electrostatic potential energy of the electron. The reducing potential energy increases the electrostatic force of attraction between the nucleus and the electron. As the energy of the electron decreases, it can no longer maintain its orbit, so it spirals in toward the proton. The frequency of the wave should be the same as the number of orbits that the electron makes each second. As the electron spirals in, it orbits faster and faster, generating electromagnetic waves of higher and higher frequency, until finally, it crashes into the proton itself and the atom collapses i.e. the atom vanishes in a fraction of second.
This means that the atom should emit light of different frequencies, starting in the red (low frequencies) and continuing to the blue (high frequencies) i.e. a continuous band of spectrum before the atom finally collapses but atoms were always found to emit the line spectra.

Since Rutherford's atomic model failed to explain the unique spectral properties of the elements and their chemical properties and moreover the stability of the atoms, the model was discarded.

Check out our other animation from here
1) List of animations
2) Thumbnail view

and please give us a feedback, it helps us to improve our software.

- Amit K. Kulshreshtha - (June 2007)
Symptoms of Smitfraud trojan and Virtumonde Spyware Pop up Ads - shown by Smitfraud - C – urging you to buy PestCapture, WinAntivirus Pro 2007 - DO NOT click on these ads
- Browser behaves erratically
- Abrupt browser and windows explorer shut down
- Slowing down of applications
- Freezing of Applications or browsers
- Instability of operating system
- Unaccounted for Internet activity
- Regular requests for DLL installations ( if you have SpyBot Teatimer running)

Pinpoint the source Run SpyBot Search and destroy, it will bring them up in its window, click on the plus icon against each name for more information about Smitfraud -C and Virtumonde worms and the files and registry entries created by them.

Removing Smitfraud - c trojan and Virtumonde adware - What works!
Removing Virtumonde
- Use Spbot to remove registry entries for virtumonde
- Files infected in Windows/ system32 folder are awvvv.dll and fccdaxu.dll, these CANNOT be deleted no matter how much you try (later we discovered many more were infected)
- Use Vundofix from Atribune - the only software that works 100% - instructions are there on the site, we are putting them here also - Download it from here

• Double-click VundoFix.exe to run it.
• When VundoFix re-opens, click the Scan for Vundo button.
• Once it's done scanning, click the Remove Vundo button.
• You will receive a prompt asking if you want to remove the files, click YES
• Once you click yes, your desktop will go blank as it starts removing Vundo.
• When completed, it will prompt that it will reboot your computer, click OK.
• Scan again on reboot and remove

Removing Smitfraud - C

Many solutions are there on the net, none of them work except this
- Use Spybot to remove all registry entries of smitfraud-C
- files infected are rpcc.dll - this CANNOT be deleted / renamed no matter how much you try
- Shut down computer
- Insert Windows XP CD and Reboot from Windows XP CD
- Let it on load on all files and once it comes to the interface of installing or repairing windows - Choose repair ( press R)
- Type your administrator password
- In the command prompt use cd.. to go back the root
- Type cd windows
- Then type cd system32
- Then type del rpcc.dll
- Then type exit
- Windows will reboot normally
- Run Spybot again to remove registry entries note rpcc.dll does not show up.
- You might have to delete this registry entry once or twice till it clears from temp files -
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Winlogon\Notify\rpcc

What did not work and tools you should have :
For virtumonde - Symantec cure FixVundo.exe did not work, it took two hours to scan all my disks and finally declared " No virtumonde found"
For virtumonde and smitfraud-c -- Deleting awvvv.dll and fccdaxu.dll or rpcc.dll ( smitfraud file) by deleting or renaming them in windows explorer,
or using command prompt and deleting them,
or starting windows in safe mode and deleting
or renaming them,
or closing all services and deleting them,
restarting windows in diagnostic mode and deleting them did not work ( same for smitfraud - c rpcc.dll)

- Smitfraud - c -
SmitRem by NoahdFear - trojan removal software did not work in our case as it could not find the files to be run in safe mode
SmitFraudFix - tool to remove Rogue applications installed with SmitFraud - did not clean - except that it started disc cleaning service, after failed cleaning operation, I stopped it coz it was taking too long.
killbox.exe : Was unable to delete the dll files
Tools you can use (For diagnosis and cleaning temporary files)
HijackThis 1.99.1 - Great tool for finding spyware, virus, trojan, and other problems CCleaner- Free tool for removing temporary files, cookies, history, and cleaning up registry problems, only check install on desktop option, otherwise embeds itself everywhere

My Story :

1) I had become more impatient - Ruled out, I had become a patient (nut case) but definitely not impatient, didn't I watch the defragmentation colors bars sorting themselves out so lovingly for 45 minutes. But Defragmenting the hard drive did not help much, yes some programs did speed up.

2) Computer had become slow - but Why? Even re-installing windows XP as an upgrade only marginally improved the performance

3) Virus attack - could be, but then what was AVG doing - making friends with it or what?

4) Malware - Yeah this could be , wait but which one ? There had been only an occasional ad embedded in internet explorer coaxing me to buy Windows Anti Virus.

What did I do to identify the sneaky pests ?

I wanted to put a name to these culprits so that I could research them on the internet. SpyBot 1.4 it was, first I updated and immunized it, then searched the root directory and lo and behold some exotic tongue twisters like Smitfraud and Virtumonde tumbled out of hidden lair. Great! now SpyBot could easily swat them Correct? Wrong, Spybot could only delete their registry entries. It could not delete some files and wanted me to restart it again on reboot, I did and even after the reboot, it could remove only the registry entries but not the dll.

I tried a number of programs, including HijackThis, Trend's online virus scanner, Panda Software's online virus scanner, Symantec's FixVundo.exe and manual instructions but to no avail! Even SpyBot Search and Destroy's software, 1 occurrences of the VirtuMonde when actually there were 16.

So now was the time to swallow my pride as a self proclaimed computer genius and cry "HELP", and so I searched all over the net, downloaded solutions, studied forums, side tracked many websites offering a quick fix till finally I could find the right cocktail to banish these two to computer hell (they come from there anyway). I have up put a series of steps above and have given more stuff on these two below. Enjoy your killing!

More on VirtuMonde :

More on Trojan Smitfraud

 

What do malware do ?

Add new desktop shortcuts or homepages: Malware can add new desktop shortcuts. Malware can redirect your default homepage to another web site.

Continuous pop ups : Offline or online Malware bombardment of popup ads continue . Malware track your financial and personal information.

 

A brief look at Malware / Spyware /

Adware / Worm / Trojans

Some adware may also fall under the category of spyware. Spyware or Trojan  is any software or malware (”malicious software”) used to spy or track your computer activity. While some spyware is legitimately and intentionally installed by parents or employers to monitor Internet activity on a computer, spyware may be installed maliciously. Often spyware may come bundled with downloads of free software or come in the form of a cookie via a web site, and this spyware may track your Internet activity or may steal secret account usernames and passwords, credit card numbers, and other personal and financial information. They may also open illicit network connections, use polymorphic tactics to self-mutate, disable security software, modify system files, and install additional malware.
Most Trojans exhibit some form of malicious, hostile, or harmful functionality or behavior. They may also severely degrade the performance and stability of your computer

 

How can you get Infected with

VirtuMonde / Smitfraud?

Web browser’s security settings may be set much too low,
You may not follow safe web browsing and email habits
You may not be regularly using a good anti-spyware application.
You might be downloading and installing Freeware or Shareware or Peer-to-Peer Software.
You might be visiting a web site that’s of questionable nature, fishy and phishy websites are swarming with Trojans, spyware, and adware, that may be automatically downloaded and installed onto your computer.

"Visual Education" as a concept means freeing education from text and making it more visual by using photographs, illustrations, animation, video and interactivity.

The major part of education has always been "textual and static", visual education can bring about a change in this system by making it more dynamic, animated, interactive and of course interesting. The changes are coming in slowly but surely in third world countries , the books that used to be in gray color a few years back are now in color. Blackboard has given way to white board with colorful markers replacing chalks. Charts are giving way to OHP in schools. But the changes are slow, definitely slow. They are awaiting the inroads to be made by computer and then links provided to Internet to usher in the new way of learning.

The question is can all that be termed as visual education ?

Yes and No, It is a proven fact that a dynamic visual transfers higher information than a textual static one. But then that is the starting point of visual education. It has to deliver knowledge in many formats to be successful. Be it color graphics or interactive animation. So Yes! those animation and graphics are visual ( text in those terms was 'visual' also ) but they do not provide education . So Visual has to be combined with education to make it worthwhile.

In lower education levels (upto K6 or class 6th) even a geographic phenomenon and simple mathematics becomes tough to understand by a child burdened with a lot of subjects being taught at school and frequently the rote or memorizing method is subscribed to. The result is tests are passed but knowledge is not gained.

Now imagine what will happen to that child in higher classes, where no longer the rote method works as subjects are vast. Most probably the child will lose interest quickly and drop out or trudge through.

Now suppose there was a method by which he could still build up his concepts and be comfortable in understanding difficult subjects. Then he might continue on with renewed interest. This method is visual education method.

Education needs to be linked with exploration to make combination deliver knowledge .

For example start off on how light creates life --- learn about photosynthesis through animation ---then about chlorophyll --- if interested find out about cholorplast ----want to know more OK--find out about how CO₂ is absorbed through interactive simulation --- then learn about electron transfer through carriers through another animation and so on.

Thus the best way to learn anything is to make it visual, interactive and curiosity based.

We have created comprehensive curiosity based science animation on our site, you can check them out from here
1) List of animations
2) Thumbnail view

and please give us a feedback, it helps us to improve our software.

 

Science and technology have a great potential for teaching and learning through animation.

Animation can visually show things that are hidden by the virtue of their size like atoms; and highlight things that are invisible like heat and light waves; can make things alive like the bacterial and amoebic life forms. Animation moreover can hold interest of the audience longer in the subject than diagrams and text can.

Animation reduces the learning time: more knowledge is acquired faster.

In the present age of e-learning, the same animation can be shared across the schools located in a city or state or continents permitting the spread of knowledge faster and easier.

Most people enjoy learning from animation. It appeals to a wide audience, independent of their age or skills. It teaches people in their natural way of learning by seeing, observing and hearing than by reading.

The combination of movement and sound creates an interesting, lively and effective method of learning. It is more appealing than text, photographs or diagrams and is therefore more likely to be remembered.

It shortens the period of experimentation illustrating in seconds, rather than days or weeks, the growth of crystals or plants.

It also reduces effort in going to field and watching a rainbow while it can be studied from desktop easily. To learn about paper production instead of receiving a mill you can see it on your computer and understand the science and technology behind it in hours

It prevents injury watching and learning to remove and discard a nuclear fuel in animation and simulation is less hazardous than and doing it in real life.

Each new innovation brings to fore a set of questions, doubts and confusions:

Are these tools of today really widespread?
Is sound necessary in learning or does it distract?
Can they substitute a teacher?
Are old methods of teaching and learning better?
Do people really learn from them?
Do long animations bore students ?
Are schools using them?
Are they being used by industry to train its workforce?
Are they effective?
Are enough available and then what is the quality aspect of these animations?
Why are there only few games for science?
Do people really enjoy them?
Why doesn't science figure in most 300 popular keywords ?
Which are the good sites that have good quality science animations on them ?
How many of these technology e-learning initiatives have really taken off?

These and many other doubts that plague the usage of new methods, but there is definitely today a need to revolutionize the whole system of learning to produce a better, faster, wider learning.

We have created comprehensive curiosity based science animation on our site, you can check them out from here
1) List of animations
2) Thumbnail view

and please give us a feedback, it helps us to improve our software.

As per Wikipedia, Communication is the activity of conveying information. This is the sole purpose of starting this article section so that we can not only convey but also get back information. The previous article section was purely one-sided with no view of audience being taken so we have modified that and introduced this newer format where you can also respond back and communicate to us your thoughts. The articles range is also being increased from purely science and technology to virtually all educational ones including management and metaphysics, this way we will cover a broader range instead of limiting ourselves to narrow fields. This section needs contribution so we are opening it to the public, you can send your articles to us and we will host them for you and good ones will win gifts from us.