DNA chips and Microarrays


A DNA microarray is an arrayed series of microscopic spots of DNA oligonucleotides, called features, where each feature contains picomoles of a specific unique sequence, such as a stretch of a gene sequence, which is used to measure the relative abundance of a sequence between samples, either differentially labelled or on different microarrays.
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These molecules are the used as probes to which only the correct target sequence will hybridise under high-stringency conditions; where the target is the labelled mix of either RNA or DNA to be analysed, in the majority of cases with a fluorophore-based detection system.
In "traditional" microarrays the probes are bound to a solid surface by covalent attachment to a chemical matrix. The solid surface can either be glass or a silicon chip, in which case they are commonly known as gene,genome chip or colloquially Affy Chip when an Affymetrix chip is used. Some recent platforms, such as Illumina, use microscopic beads, instead of the large solid support (glass or treated silicon) present in traditional microarrays. DNA arrays are different from other types of microarray only in that they either measure DNA or use DNA as part of its detection system. DNA arrays are commonly used for expression profiling, i.e., monitoring expression levels of thousands of genes simultaneously, or for comparative genomic hybridization.
Types of Array
Arrays of DNA can either be spatially arranged, as in the commonly known gene or genome chip, DNA chip, or gene array, or can be specific DNA sequences tagged or labelled such that they can be independently identified in solution. The traditional solid-phase array is a collection of microscopic DNA spots attached to a solid surface, such as glass, plastic or silicon chip. The affixed DNA segments are known as probes (although some sources will use different nomenclature such as reporters), thousands of which can be placed in known locations on a single DNA microarray. Microarray technology evolved from Southern blotting, whereby fragmented DNA is attached to a substrate and then probed with a known gene or fragment. DNA microarrays can be used to detect DNA (e.g., in comparative genomic hybridization); it also permits detection of RNA (most commonly as cDNA after reverse transcription) that may or may not be translated into proteins, which is referred to as "expression analysis" or expression profiling.

Since there can be tens of thousands of distinct probes on an array, each microarray experiment can potentially accomplish the equivalent number of genetic tests in parallel. Arrays have therefore dramatically accelerated many types of investigations. The use of a collection of distinct DNAs in arrays for expression profiling was first described in 1987, and the arrayed DNAs were used to identify genes whose expression is modulated by interferon. These early gene arrays were made by spotting cDNAs onto filter paper with a pin-spotting device. The use of miniaturized microarrays for gene expression profiling was first reported in 1995, and a complete eukaryotic genome (Saccharomyces cerevisiae) on a microarray was published in 1997. Fabrication Spotted vs. oligonucleotide arrays
Microarrays can be fabricated using a variety of technologies, including printing with fine-pointed pins onto glass slides, photolithography using pre-made masks, photolithography using dynamic micromirror devices, ink-jet printing, or electrochemistry on microelectrode arrays.
In spotted microarrays, the probes are oligonucleotides, cDNA or small fragments of PCR products that correspond to mRNAs. The probes are synthesized prior to deposition on the array surface and are then "spotted" onto glass. A common approach utilizes an array of fine pins or needles controlled by a robotic arm that is dipped into wells containing DNA probes and then depositing each probe at designated locations on the array surface. The resulting "grid" of probes represents the nucleic acid profiles of the prepared probes and is ready to receive complementary cDNA or cRNA "targets" derived from experimental or clinical samples. This technique is used by research scientists around the world to produce "in-house" printed microarrays from their own labs. These arrays may be easily customized for each experiment, because researchers can choose the probes and printing locations on the arrays, synthesize the probes in their own lab (or collaborating facility), and spot the arrays. They can then generate their own labeled samples for hybridization, hybridize the samples to the array, and finally scan the arrays with their own equipment. This provides a relatively low-cost microarray that is customized for each study, and avoids the costs of purchasing often more expensive commercial arrays that may represent vast numbers of genes that are not of interest to the investigator. Publications exist which indicate in-house spotted microarrays may not provide the same level of sensitivity compared to commercial oligonucleotide arrays, possibly owing to the small batch sizes and reduced printing efficiencies when compared to industrial manufactures of oligo arrays. Applied Microarrays offers a commercial array platform called the "CodeLink" system where 30-mer oligonucleotide probes (sequences of 30 nucleotides in length) are piezoelectrically deposited on an acrylamide matrix without any contact being made between the depositing equipment and the array surface itself. These arrays are comparable in quality to most manufactured arrays and generally superior to in-house printed arrays.
In oligonucleotide microarrays, the probes are short sequences designed to match parts of the sequence of known or predicted open reading frames. Although oligonucleotide probes are often used in "spotted" microarrays, the term "oligonucleotide array" most often refers to a specific technique of manufacturing. Oligonucleotide arrays are produced by printing short oligonucleotide sequences designed to represent a single gene or family of gene splice-variants by synthesizing this sequence directly onto the array surface instead of depositing intact sequences. Sequences may be longer (60-mer probes such as the Agilent design) or shorter (25-mer probes produced by Affymetrix) depending on the desired purpose; longer probes are more specific to individual target genes, shorter probes may be spotted in higher density across the array and are cheaper to manufacture. One technique used to produce oligonucleotide arrays include photolithographic synthesis (Agilent and Affymetrix) on a silica substrate where light and light-sensitive masking agents are used to "build" a sequence one nucleotide at a time across the entire array. Each applicable probe is selectively "unmasked" prior to bathing the array in a solution of a single nucleotide, then a masking reaction takes place and the next set of probes are unmasked in preparation for a different nucleotide exposure. After many repetitions, the sequences of every probe become fully constructed. More recently, Maskless Array Synthesis from NimbleGen Systems has combined flexibility with large numbers of probes.
Two-color vs. one-color detection
Two-Color microarrays or Two-Channel microarrays are typically hybridized with cDNA prepared from two samples to be compared (e.g. diseased tissue versus healthy tissue) and that are labeled with two different fluorophores. Fluorescent dyes commonly used for cDNA labelling include Cy3, which has a fluorescence emission wavelength of 570 nm (corresponding to the green part of the light spectrum), and Cy5 with a fluorescence emission wavelength of 670 nm (corresponding to the red part of the light spectrum). The two Cy-labelled cDNA samples are mixed and hybridized to a single microarray that is then scanned in a microarray scanner to visualize fluorescence of the two fluorophores after excitation with a laser beam of a defined wavelength. Relative intensities of each fluorophore may then be used in ratio-based analysis to identify up-regulated and down-regulated genes.
Oligonucleotide microarrays often contain control probes designed to hybridize with RNA spike-ins. The degree of hybridization between the spike-ins and the control probes is used to normalize the hybridization measurements for the target probes. Although absolute levels of gene expression may be determined in the two-color array, the relative differences in expression among different spots within a sample and between samples is the preferred method of data analysis for the two-color system. Examples of providers for such microarrays includes Agilent with their Dual-Mode platform, Eppendorf with their DualChip platform for fluorescence labeling, and TeleChem International with Arrayit.
In single-channel microarrays or one-color microarrays, the arrays are designed to give estimations of the absolute levels of gene expression. Therefore the comparison of two conditions requires two separate single-dye hybridizations. As only a single dye is used, the data collected represent absolute values of gene expression. These may be compared to other genes within a sample or to reference "normalizing" probes used to calibrate data across the entire array and across multiple arrays. Three popular single-channel systems are the Affymetrix "Gene Chip", the Applied Microarrays "CodeLink" arrays, and the Eppendorf "DualChip & Silverquant". One strength of the single-dye system lies in the fact that an aberrant sample cannot affect the raw data derived from other samples, because each array chip is exposed to only one sample (as opposed to a two-color system in which a single low-quality sample may drastically impinge on overall data precision even if the other sample was of high quality). Another benefit is that data are more easily compared to arrays from different experiments; the absolute values of gene expression may be compared between studies conducted months or years apart. A drawback to the one-color system is that, when compared to the two-color system, twice as many microarrays are needed to compare samples within an experiment.

Electron Transport in Mitochondria

The cells of almost all eukaryotes contain intracellular organelles called mitochondria, which produce ATP. Energy sources such as glucose are initially metabolized in the cytoplasm. The products are imported into mitochondria. Mitochondria continue the process of catabolism using metabolic pathways including the Krebs cycle, fatty acid oxidation, and amino acid oxidation.
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The end result of these pathways is the production of two kinds of energy-rich electron donors, NADH and succinate. Electrons from these donors are passed through an electron transport chain to oxygen, which is reduced to water. This is a multi-step redox process that occurs on the mitochondrial inner membrane. The enzymes that catalyze these reactions have the ability to simultaneously create a proton gradient across the membrane, producing a thermodynamically unlikely high-energy state with the potential to do work. Although electron transport occurs with great efficiency, a small percentage of electrons are prematurely leaked to oxygen, resulting in the formation of the toxic free-radical superoxide.

The similarity between intracellular mitochondria and free-living bacteria is striking. The known structural, functional, and DNA similarities between mitochondria and bacteria provide strong evidence that mitochondria evolved from intracellular bacterial symbionts


Four membrane-bound complexes have been identified in mitochondria. Each is an extremely complex transmembrane structure that is embedded in the inner membrane. Three of them are proton pumps. The structures are electrically connected by lipid-soluble electron carriers and water-soluble electron carriers.



Complex I

Complex I (NADH dehydrogenase, also called NADH:ubiquinone oxidoreductase; EC 1.6.5.3) removes two electrons from NADH and transfers them to a lipid-soluble carrier, ubiquinone (Q). The reduced product, ubiquinol (QH2) is free to diffuse within the membrane. At the same time, Complex I moves four protons (H+) across the membrane, producing a proton gradient. Complex I is one of the main sites at which premature electron leakage to oxygen occurs, thus being one of main sites of production of a harmful free radical called superoxide.

The pathway of electrons occurs as follows:

NADH is oxidized to NAD+, reducing Flavin mononucleotide to FMNH2 in one two-electron step. The next electron carrier is a Fe-S cluster, which can only accept one electron at a time to reduce the ferric ion into a ferrous ion. In a convenient manner, FMNH2 can be oxidized in only two one-electron steps, through a semiquinone intermediate. The electron thus travels from the FMNH2 to the Fe-S cluster, then from the Fe-S cluster to the oxidized Q to give the free-radical (semiquinone) form of Q. This happens again to reduce the semiquinone form to the ubiquinol form, QH2. During this process, four protons are translocated across the inner mitochondrial membrane, from the matrix to the intermembrane space. This creates a proton gradient that will be later used to generate ATP through oxidative phosphorylation.


Complex II

Complex II (succinate dehydrogenase; EC 1.3.5.1) is not a proton pump. It serves to funnel additional electrons into the quinone pool (Q) by removing electrons from succinate and transferring them (via FAD) to Q. Complex II consists of four protein subunits: SDHA,SDHB,SDHC, and SDHD. Other electron donors (e.g., fatty acids and glycerol 3-phosphate) also funnel electrons into Q (via FAD), again without producing a proton gradient.

Complex III

Complex III (cytochrome bc1 complex; EC 1.10.2.2) removes in a stepwise fashion two electrons from QH2 at the QO site and sequentially transfers them to two molecules of cytochrome c, a water-soluble electron carrier located within the intermembrane space. The two other electrons are sequentially passed across the protein to the Qi site where quinone part of ubiquinone is reduced to quinol. A proton gradient is formed because it takes 2 quinol (4H+4e-) oxidations at the Qo site to form one quinol (2H+2e-) at the Qi site. (in total 6 protons: 2 protons reduce quinone to quinol and 4 protons are released from 2 ubiquinol). The bc1 complex does NOT 'pump' protons, it helps build the proton gradient by an asymmetric absorption/release of protons.

When electron transfer is hindered (by a high membrane potential, point mutations or respiratory inhibitors such as antimycin A), Complex III may leak electrons to oxygen resulting in the formation of superoxide, a highly-toxic species, which is thought to contribute to the pathology of a number of diseases, including aging.


Complex IV

Complex IV (cytochrome c oxidase; EC 1.9.3.1) removes four electrons from four molecules of cytochrome c and transfers them to molecular oxygen (O2), producing two molecules of water (H2O). At the same time, it moves four protons across the membrane, producing a proton gradient.



Coupling with oxidative phosphorylation

The chemiosmotic coupling hypothesis, as proposed by Nobel Prize in Chemistry winner Peter D. Mitchell, explains that the electron transport chain and oxidative phosphorylation are coupled by a proton gradient across the inner mitochondrial membrane. The efflux of protons creates both a pH gradient and an electrochemical gradient. This proton gradient is used by the FOF1 ATP synthase complex to make ATP via oxidative phosphorylation. ATP synthase is sometimes regarded as complex V of the electron transport chain. The FO component of ATP synthase acts as an ion channel for return of protons back to mitochondrial matrix. During their return, the free energy produced during the generation of the oxidized forms of the electron carriers (NAD+ and Q) is released. This energy is used to drive ATP synthesis, catalyzed by the F1 component of the complex.
Coupling with oxidative phosphorylation is a key step for ATP production. However, in certain cases, uncoupling may be biologically useful. The inner mitochondrial membrane of brown adipose tissue contains a large amount of thermogenin (an uncoupling protein), which acts as uncoupler by forming an alternative pathway for the flow of protons back to matrix. This results in consumption of energy in thermogenesis rather than ATP production. This may be useful in cases when heat production is required, for example in colds or during arise of hibernating animals. Synthetic uncouplers (e.g., 2,4-dinitrophenol) also exist, and, at high doses, are lethal.


Summary

The mitochondrial electron transport chain removes electrons from an electron donor (NADH or QH2) and passes them to a terminal electron acceptor (O2) via a series of redox reactions. These reactions are coupled to the creation of a proton gradient across the mitochondrial inner membrane. There are three proton pumps: I, III, and IV. The resulting transmembrane proton gradient is used to make ATP via ATP synthase.

The reactions catalyzed by Complex I and Complex III exist roughly at equilibrium. This means that these reactions are readily reversible, simply by increasing the concentration of the products relative to the concentration of the reactants (for example, by increasing the proton gradient). ATP synthase is also readily reversible. Thus ATP can be used to make a proton gradient, which in turn can be used to make NADH. This process of reverse electron transport is important in many prokaryotic electron transport chains.

Electron transport chain. (2009, September 7). In Wikipedia, The Free Encyclopedia. Retrieved 21:19, September 7, 2009, from http://en.wikipedia.org/w/index.php?title=Electron_transport_chain&oldid=312464432

MicroRNA Animation

MicroRNAs (miRNA) are single-stranded RNA molecules of about 21-23 nucleotides in length, which regulate gene expression. miRNAs are encoded by genes that are transcribed from DNA but not translated into protein (non-coding RNA); instead they are processed from primary transcripts known as pri-miRNA to short stem-loop structures called pre-miRNA and finally to functional miRNA. Mature miRNA molecules are partially complementary to one or more messenger RNA (mRNA) molecules, and their main function is to downregulate gene expression. They were first described in 1993 by Lee and colleagues , yet the term microRNA was only introduced in 2001 in a set of three articles in Science (26 October 2001)

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Formation and processing
The genes encoding miRNAs are much longer than the processed mature miRNA molecule; miRNAs are first transcribed as primary transcripts or pri-miRNA with a cap and poly-A tail and processed to short, 70-nucleotide stem-loop structures known as pre-miRNA in the cell nucleus. This processing is performed in animals by a protein complex known as the Microprocessor complex, consisting of the nuclease Drosha and the double-stranded RNA binding protein Pasha. These pre-miRNAs are then processed to mature miRNAs in the cytoplasm by interaction with the endonuclease Dicer, which also initiates the formation of the RNA-induced silencing complex (RISC). This complex is responsible for the gene silencing observed due to miRNA expression and RNA interference. The pathway in plants varies slightly due to their lack of Drosha homologs; instead, Dicer homologs alone effect several processing steps.
Most pre-miRNAs don't have a perfect double-stranded RNA (dsRNA) structure topped by a terminal loop. There are few possible explanations for such selectivity. One could be that dsRNAs longer than 21 base pairs activate interferon response and anti-viral machinery in the cell. Another plausible explanation could be that thermodynamical profile of pre-miRNA determines which strand will be incorporated into Dicer complex. Indeed, aforementioned study by Han et al. demonstrated very clear similarities between pri-miRNAs encoded in respective (5'- or 3'-) strands.
When Dicer cleaves the pre-miRNA stem-loop, two complementary short RNA molecules are formed, but only one is integrated into the RISC complex. This strand is known as the guide strand and is selected by the argonaute protein, the catalytically active RNase in the RISC complex, on the basis of the stability of the 5' end. The remaining strand, known as the anti-guide or passenger strand, is degraded as a RISC complex substrate. After integration into the active RISC complex, miRNAs base pair with their complementary mRNA molecules and induce mRNA degradation by argonaute proteins, the catalytically active members of the RISC complex. It is as yet unclear how the activated RISC complex locates the mRNA targets in the cell, though it has been shown that the process is not coupled to ongoing protein translation from the mRNA

Cellular functions


The function of miRNAs appears to be in gene regulation. For that purpose, a miRNA is complementary to a part of one or more messenger RNAs (mRNAs). Animal miRNAs are usually complementary to a site in the 3' UTR whereas plant miRNAs are usually complementary to coding regions of mRNAs. The annealing of the miRNA to the mRNA then inhibits protein translation, but sometimes facilitates cleavage of the mRNA. This is thought to be the primary mode of action of plant miRNAs. In such cases, the formation of the double-stranded RNA through the binding of the miRNA triggers the degradation of the mRNA transcript through a process similar to RNA interference (RNAi), though in other cases it is believed that the miRNA complex blocks the protein translation machinery or otherwise prevents protein translation without causing the mRNA to be degraded. miRNAs may also target methylation of genomic sites which correspond to targeted mRNAs. miRNAs function in association with a complement of proteins collectively termed the miRNP.
This effect was first described for the worm C. elegans in 1993 by Victor Ambros and coworkers (Lee et al., 1993). As of 2002, miRNAs have been confirmed in various plants and animals, including C. elegans, human and the plant Arabidopsis thaliana. Genes have been found in bacteria that are similar in the sense that they control mRNA abundance or translation by binding an mRNA by base pairing, however they are not generally considered to be miRNAs because the Dicer enzyme is not involved.
In plants, similar RNA species termed short-interfering RNAs siRNAs are used to prevent the transcription of viral RNA. While this siRNA is double-stranded, the mechanism seems to be closely related to that of miRNA, especially taking the hairpin structures into account. siRNAs are also used to regulate cellular genes, as miRNAs do.
Detecting and manipulating miRNA signalling
The activity of an miRNA can be experimentally blocked using a locked nucleic acid oligo, a Morpholino oligo or a 2'-O-methyl RNA oligo. Steps in the maturation of miRNAs can be blocked by steric-blocking oligos. The target site of an miRNA on an mRNA can be blocked by a steric blocking oligo
miRNA and cancer

miRNA has been found to have links with some types of cancer.

A study of mice altered to produce excess c-myc — a protein implicated in several cancers — shows that miRNA has an effect on the development of cancer. Mice that were engineered to produce a surplus of types of miRNA found in lymphoma cells developed the disease within 50 days and died two weeks later. In contrast, mice without the surplus miRNA lived over 100 days.

Another study found that two types of miRNA inhibit the E2F1 protein, which regulates cell proliferation. miRNA appears to bind to messenger RNA before it can be translated to proteins that switch genes on and off.

By measuring activity among 217 genes encoding miRNA, patterns of gene activity that can distinguish types of cancers can be discerned. miRNA signatures may enable classification of cancer. This will allow doctors to determine the original tissue type which spawned a cancer and to be able to target a treatment course based on the original tissue type. miRNA profiling has already been able to determine whether patients with chronic lymphocytic leukemia had slow growing or aggressive forms of the cancer

miRNA and heart disease

miRNA has been shown to be related to heart disease. Mice were created that were deficient in a muscle-specific miRNA and these mice had high rate of the most common congenital heart disease -- ventricular septal defects characterized by the holes between the left and the right ventricles of the heart. Such mice also show hyperplasia (an increase of the number of cardiac muscle cells that leads to heart enlargement) and abnormalities in cardiac conduction.

Stroke Animation

Stroke or cerebrovascular accident (CVA) is the rapidly developing loss of brain functions due to a disturbance in the blood vessels supplying blood to the brain. This can be due to ischemia (lack of blood supply) caused by thrombosis or embolism, or due to a hemorrhage. In medicine, a stroke, fit, or faint is sometimes referred to as an ictus [cerebri], from the Latin icere ("to strike"), especially prior to a definitive diagnosis.
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Stroke is a medical emergency and can cause permanent neurological damage, complications and death if not promptly diagnosed and treated. It is the third leading cause of death and the leading cause of adult disability in the United States and Europe. It is predicted that stroke will soon become the leading cause of death worldwide. Risk factors for stroke include advanced age, hypertension (high blood pressure), previous stroke or transient ischaemic attack (TIA), diabetes, high cholesterol, cigarette smoking, atrial fibrillation, migraine with aura, and thrombophilia (a tendency to thrombosis). Blood pressure is the most important modifiable risk factor of stroke.

The traditional definition of stroke, devised by the World Health Organisation in the 1970s, is a "neurological deficit of cerebrovascular cause that persists beyond 24 hours or is interrupted by death within 24 hours". This definition was supposed to reflect the reversibility of tissue damage and was devised for the purpose, with the time frame of 24 hours being chosen arbitrarily. It divides stroke from TIA, which is a related syndrome of stroke symptoms that resolve completely within 24 hours. With the availability of treatments that, when given early, can reduce stroke severity, many now prefer alternative concepts, such as brain attack and acute ischemic cerebrovascular syndrome (modeled after heart attack and acute coronary syndrome respectively), that reflect the urgency of stroke symptoms and the need to act swiftly.

Treatment of stroke is occasionally with thrombolysis ("clot buster"), but usually with supportive care (physiotherapy and occupational therapy) and secondary prevention with antiplatelet drugs (aspirin and often dipyridamole), blood pressure control, statins and anticoagulation


Thrombotic stroke

In thrombotic stroke, a thrombus (blood clot) usually forms around atherosclerotic plaques. Since blockage of the artery is gradual, onset of symptomatic thrombotic strokes is slower. A thrombus itself (even if non-occluding) can lead to an embolic stroke (see below) if the thrombus breaks off, at which point it is called an "embolus". Thrombotic stroke can be divided into two types depending on the type of vessel the thrombus is formed on:
Large vessel disease involves the common and internal carotids, vertebral, and the Circle of Willis. Diseases that may form thrombi in the large vessels include (in descending incidence): atherosclerosis, vasoconstriction (tightening of the artery), aortic, carotid or vertebral artery dissection, various inflammatory diseases of the blood vessel wall (Takayasu arteritis, giant cell arteritis, vasculitis), noninflammatory vasculopathy, Moyamoya disease and fibromuscular dysplasia
Small vessel disease involves the smaller arteries inside the brain: branches of the circle of Willis, middle cerebral artery, stem, and arteries arising from the distal vertebral and basilar artery. Diseases that may form thrombi in the small vessels include (in descending incidence): lipohyalinosis (build-up of fatty hyaline matter in the blood vessel as a result of high blood pressure and aging) and fibrinoid degeneration (stroke involving these vessels are known as lacunar infarcts) and microatheroma (small atherosclerotic plaques).
Embolic stroke

Embolic stroke refers to the blockage of an artery by an embolus, a traveling particle or debris in the arterial bloodstream originating from elsewhere. An embolus is most frequently a thrombus, but it can also be a number of other substances including fat (e.g. from bone marrow in a broken bone), air, cancer cells or clumps of bacteria (usually from infectious endocarditis).

Because an embolus arises from elsewhere, local therapy only solves the problem temporarily. Thus, the source of the embolus must be identified. Because the embolic blockage is sudden in onset, symptoms usually are maximal at start. Also, symptoms may be transient as the embolus is partially resorbed and moves to a different location or dissipates altogether.

Emboli most commonly arise from the heart (especially in atrial fibrillation) but may originate from elsewhere in the arterial tree. In paradoxical embolism, a deep vein thrombosis embolises through an atrial or ventricular septal defect in the heart into the brain.

Cycle Sequencing


To sequence a piece of dna you need 1)a Template DNA 2) a short DNA primer that is complementary to the dna you want to sequence, 3)A enzyme called DNA polymerase,(4) Four nucleotides.(A,C,G,T), To this mix ,we also add a second type of nucleotide; one that has a slightly different chemical formula, These dideoxynucleotides(diddtp) can be recognized by a DNA sequencer.
To start the sequencing reaction this mixture is heated to 96C ,so the template DNA's two complementary strand separates,Then the temperature is lowered, so that the short "primer" sequence finds its complementary sequence in the template DNA.Finally the temperature is raised 60c,this allows the enzyme to bind to the DNA and create a new strand of DNA.
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The sequence of this new DNA is complementary to the original DNA strand. The enzyme makes no distinction between dNTPs or didNTPs.each time a didNTP is incorporated, in this case didATP,The synthesis stops. Because billion of DNA molecules are present in the test tube, the strand can be terminated at any position. This results in collection of DNA strands of many different lengths.
The sequencing reaction is transferred from the test tube to a lane of a polyacrylamide gel. The gel is placed into a DNA sequencer for electrophoresis and analysis. The fragments migrate according to size and each is detected as it passes a laser beam at the bottom of the gel. Each type of dideoxynucleotide emits colored light of a characteristic wavelength and is recorded as a colored band on a simulated gel image, and finally computer program interprets the raw data and outputs an electropherogram with colored peaks representing each letter in the sequence.the sequence fragments are sorted out according to the size, starting from the shortest to longest one, the stimulated gel image is read from bottom to top, starting with the smallest fragment, Thus we sequences present in template DNA.

Electroencephalograph(EEG) Animation


Brain waves recorded from the scalp prove that human beings never "switch off" their minds. Here three levels of arousal--sleeping, relaxing and action--all have a characteristic brain wave pattern. The machine used to monitor and record this activity is an electroencephalograph or EEG. In deep sleep, the EEG pattern produces large, slow waves. When relaxing the waves become faster. In an active situation the EEG is very dense and is described as having a low voltage and a high frequency, which produce a fast wave.
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Spleen Animation


The spleen is a small organ located behind the stomach in the left, upper part of the abdomen. A mass of lymphoid tissue, it contains two distinct areas, the white pulp and the red pulp. The white pulp is distributed, as tiny nodules of lymphatic tissue, among the red pulp, which fills all the remaining space. The white pulp is responsible for the production of lymphocytes. Some lymphocytes enter the blood, while others remain in the spleen, where they ingest and destroy foreign or damaged cells. The red pulp contains many blood channels, expanded capillary lakes, which act as filters when blood is forced through them, removing damaged or abnormal red cells and allowing normal ones to pass through. The lymphocytes then engulf and destroy these damaged red cells. The spleen also acts as a store for red blood cells.
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Vaccination

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Pizza Skin Syndrome

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Biochemical pathway


A series of chemical reactions occurring within a cell. In each pathway, a principal chemical is modified by chemical reactions. Enzymes catalyze these reactions, and often require dietary minerals, vitamins and other cofactors in order to function properly. Because of the many chemicals that may be involved, pathways can be quite elaborate. In addition, many pathways can exist within a cell.


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Organisms contain many different kinds of enzymes that catalyze a variety of different reactions. many of these reactions, such as those involved in the biosynthesis of an amino acid are carried out in a specific sequence called biochemical pathway.
In such pathways, a substrate is converted into a product by te first enzyme in the pathway and the product of the first reaction then becomes the substrate for the next reaction. The sequence of reactions continues until the final product is made.
when a biochemical pathway is functioning, the initial substrate is continually converted to the final product through the series of steps in the pathway

Mirror Neuron Hypothesis of Autism





Marco Iacoboni, M.D., Ph.D. discusses the mirror neuron hypothesis of autism which suggests that reduced mirror neuron activity may be a central feature of autism. Mirror neurons are cells concerned with motor behavior and are considered neural precursors of neural systems concerned with language and social interactions

A Delicate Balance: Stem Cells Cancer and Immune Response



Vitamins and Supplements: Vital or Superfluous?





Explore measures that can be taken to not only live longer but also live better with UCSF's Dr. Donald Abrams who discusses vitamins and supplements.

Psychosocial Aspects of Chronic Pain

The UCSD School of Medicine and the Diana Padelford Binkley Foundation bring you the newest installments of this innovative series targeted at successfully managing pain in women. Studies show women often receive inadequate care as pain manifests uniquely in the sexes and requires distinctive treatment strategies. In this program, Melanie A. Greenberg, Ph.D., a leading expert from Alliant International University, talks about the psychosocial fallout due to chronic pain.

Rheumatoid Arthritis Lecture

Rheumatoid arthritis affects 1.3 million Americans. Research advances and drug development have helped control this chronic disease. Noted UCLA Rheumatology expert Dr. Michael Weisman, presents an update on the latest treatments in the first of two lectures.
Part One





Part 2

Pain and the Musculoskeletal

The UCSD School of Medicine and the Diana Padelford Binkley Foundation bring you the newest installments of this innovative series targeted at successfully managing pain in women. Studies show women often receive inadequate care as pain manifests uniquely in the sexes and requires distinctive treatment strategies. In this program, Mark Young, M.D., national expert with University of Maryland, talks about pain and the musculoskeletal system and the impact of gender. Series: Pain Management in Women Over the Lifecycle





Natural Supplements for Pain in Women

The UCSD School of Medicine and the Diana Padelford Binkley Foundation bring you the newest installments of this innovative series targeted at successfully managing pain in women. Studies show women often receive inadequate care as pain manifests uniquely in the sexes and requires distinctive treatment strategies. In this program, Robert Bonakdar, M.D., Director of Pain Management, Scripps Center for Integrative Medicine, talks about natural supplements for treating pain in women. Series:


Sexual Dimorphism in Pain Syndromes




The UCSD School of Medicine and the Diana Padelford Binkley Foundation bring you the newest installments of this innovative series targeted at successfully managing pain in women. Studies show women often receive inadequate care as pain manifests uniquely in the sexes and requires distinctive treatment strategies. In this program, Jon Levine, M.D., a leading expert from UC San Francisco, talks about the differences in pain syndromes and responses to pain medications in women and men.

Holliday Junction



Emerging Infections

Emerging Infections



UCSD Professor Emeritus Dr. John Holland discusses emerging infections around the globe - from mad cow disease to new strains of common viruses

Experiments in Consciousness by Francis Crick

Join Nobel Laureate Francis Crick as he explains new ideas and experiments in the fascinating field of human consciousness.


Healing Bone Fracture


From the Big Bang to Irreducible Complexity

This program from the Focus on Origns series features an exclusive interview with Dr. Michael Behe, author of Darwin's Black Box: The Biochemical Challenge to Evolution. Dr. Behe discusses a number of inferences to intelligent design including the Big Bang, the fine using of the Cosmos, irreducibly complex molecular machines, and the ability of natural selection to inhibit major evolutionary change.


The Retinal Blind Spot in the Vision of our Origins


AutoDock4 Installation

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
To run AutoDock on Windows, you must first download and install Cygwin, a Linux-like environment for Windows. Cygwin is available from http://www.cygwin.com. Follow the instructions for installing and setting up Cygwin from the Cygwin web site.

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Cygwin installation:
  • Go to Cygwin website http://www.cygwin.com/.
  • Download setup.exe.
  • Open setup.exe(Choose run)
  • Choose Next.
  • Choose Install from Internet option.
  • Choose Root Directory(D or E recommended).
  • Direct Connection.
  • Choose the any mirror sites.
  • Select default settings.
  • This will install Cygwin in your PC.
Auto Dock4



AutoDock can be downloaded from http://autodock.scripps.edu/downloads .



ADT
ADT can be downloaded from http://mgltools.scripps.edu/downloads 


Install ADT

Installing Autodock
  • Go to Start->Program Files->Cygwin->Cygwin Bash Shell
  • Type whoami (to find system name).
  • cd /cygdrive/c/Documents\ and\ Settings/YOUR_USERNAME/Desktop.
  • Extracting autodock4 tar xvzf autodocksuite-4.0.1-i86Cygwin.tar.gz
  • cd i86Cygwin
cp autodock4.exe /usr/local/bin     cp autogrid4.exe /usr/local/bin

Insulin Resistance


Neuroscientist Charles F. Stevens


Sick Building Syndrome


Ethical Implications of the Genome Era


Sexuality Aging and Dementia


Understanding the Anatomy Behind Clinical Procedures


Kidney Transplant Update: Humoral Rejections; New Drugs

Kidney Transplant Update presents Dr. Julie Yabu on strategies in the treatment of humoral rejection and Dr. Flavio Vincenti on new drugs in the pipeline. UCSF is one of the premier centers in abdominal organ Transplantation. This annual update is shares the current new knowledge with healthcare workers who deal with transplantation issues.


Oncology 101 and Colon Cancer in 2008

Dr. Andrew Ko of the UCSF Comprehensive Cancer Center explores how research and advances in technologies are impacting clinical care of colon cancer. Ko's research is in the development of new treatment strategies, including molecularly targeted therapies, for patients with gastrointestinal malignancies. Series: UCSF Mini Medical School for the Public


Membrane Potential