Sunday, September 14, 2008
Wednesday, September 3, 2008
Cloned items in food supply?
Washington: Food and milk from the offspring of cloned animals may have entered the US food supply, the US government said on Tuesday, but its impossible to know because there is no difference between cloned and conventional products.
The US Food and Drug Administration said in January meat and milk from cloned cattle, swine and goats and their offspring were as safe as products from traditional animals. Before then, farmers and ranchers had followed a voluntary moratorium on the sale of clones and their offspring.
While the FDA evaluated the safety of food from clones and their offspring, the agriculture department was in charge of managing the transition of these animals into the food supply.
“It is theoretically possible” offspring from clones are in the food supply, said Siobhan De-Lancey, an FDA spokeswoman.
There are an estimated 600 cloned animals in the US. Proponents say that cloning is a way to create more disease-resistant animals that produce more milk and better meat.
The cloning industry and the FDA say cloned animals and their offspring are as safe as their traditional counterparts.
Critics contend not enough is known about the technology to ensure it is safe, and say the FDA needs to address concerns over animal cruelty and ethical issues. “It worries me that this technology is out of control in so many ways,” said Charles Margulis, a spokesman with the Center for Environmental Health.
FDA and USDA said it is impossible to differentiate between cloned animals, their offspring and conventionally bred animals, making it difficult to know if offspring are in the food supply.
“But they would be a very limited number because of the very few number of clones that are out there and relatively few of those clones are at an age where they would be parenting,” said Bruce Knight, USDA’s undersecretary for marketing and regulatory programs.
Major food companies including Tyson Foods Inc, the largest US meat company, and Smithfield Foods Inc have said that they would avoid using cloned animals because of safety concerns. REUTERS
Brain protein holds key to fertility, say scientists
Dubbed kisspeptin, the protein is known to play a vital role in kick-starting puberty.
Now, a group from the University of Otago led by Professor Allan Herbison, in collaboration with Cambridge University researchers, has published the first evidence that kisspeptin signalling in the brain is also essential for ovulation to occur in adults.
Studying female mice, the researchers found that signalling between kisspeptin and its cell receptor GPR54 was essential to activate gonadotrophin-releasing hormone (Gn-RH) neurons, the nerve cells known to initiate ovulation.
The research appears in the latest issue of the Journal of Neuroscience. “This is an exciting finding, as people have been trying to find out precisely how the brain controls ovulation for more than 30 years. This work now reveals a crucial link in the brain circuitry responsible,” Herbison said in a statement. REUTERS
Friday, August 29, 2008
Electrophoretic mobility shift assay
Principle
A mobility shift assay generally involves electrophoretic separation of a protein-DNA or protein-RNA mixture on a polyacrylamide or agarose gel for a short period (about 1.5-2 hr for a 15- to 20-cm gel). [3] The speed at which different molecules (and combinations thereof) move through the gel is determined by their size and charge, and to a lesser extent, their shape (see gel electrophoresis). The control lane (DNA probe without protein present) will contain a single band corresponding to the unbound DNA or RNA fragment. However, assuming that the protein is capable of binding to the fragment, the lane with protein present will contain another band that represents the larger, less mobile complex of nucleic acid probe bound to protein which is 'shifted' up on the gel (since it has moved more slowly).
Under the correct experimental conditions, the interaction between the DNA and protein is stabilized and the ratio of bound to unbound nucleic acid on the gel reflects the fraction of free and bound probe molecules as the binding reaction enters the gel. This stability is in part due to the low ionic strength of the buffer, but also due to a "caging effect", in that the protein, surrounded by the gel matrix, is unable to diffuse away from the probe before they recombine. If the starting concentrations of protein and probe are known, the affinity of the protein for the nucleic acid sequence may be determined. If the protein concentration is not known, it can be determined by increasing the concentration of DNA probe until further increments do not increase the fraction of protein bound. By comparison with a set of standard dilutions of free probe run on the same gel, the number of moles of protein can be calculated. [3]
An antibody that recognizes the protein can be added to this mixture to create an even larger complex with a greater shift. This method is referred to as a supershift assay, and is used to unambiguously identify a protein present in the protein-nucleic acid complex.
Often, an extra lane is run with a competitor oligonucleotide to determine the most favorable binding sequence for the binding protein. The use of different oligonucleotides of defined sequence allows the identification of the precise binding site by competition (not shown in diagram). Variants of the competition assay are useful for measuring the specificity of binding and for measurement of association and dissociation kinetics.
For visualization purposes, the nucleic acid fragment is usually labeled with a radioactive, fluorescent or biotin label. Standard ethidium bromide staining is less sensitive than these methods and can lack the sensitivity to detect the nucleic acid if small amounts are used in these experiments. When using a biotin label, streptavidin conjugated to an enzyme such as horseradish peroxidase is used to detect the DNA fragment (Non-radioactive EMSA review).
Wednesday, August 27, 2008
Cell Membrane






Cell membrane
From Wikipedia, the free encyclopedia
The cell membrane (also called the plasma membrane, plasmalemma, or "phospholipid bilayer") is a selectively permeablelipid bilayer found in all cells.[1] It contains a wide variety of biological molecules, primarily proteins and lipids, which are involved in a vast array of cellular processes such as cell adhesion, ion channel conductance and cell signaling. The plasma membrane also serves as the attachment point for both the intracellular cytoskeleton and, if present, the cell wall.
Function
The cell membrane surrounds the cytoplasm of a cell and, in animal cells, physically separates the intracellular components from the extracellular environment, thereby serving a function similar to that of skin. In fungi, some bacteria, and plants, an additional cell wall forms the outermost boundary; however, the cell wall plays mostly a mechanical support role rather than a role as a selective boundary. The cell membrane also plays a role in anchoring the cytoskeleton to provide shape to the cell, and in attaching to the extracellular matrix to help group cells together in the formation of tissues.
The barrier is selectively permeable and able to regulate what enters and exits the cell, thus facilitating the transport of materials needed for survival. The movement of substances across the membrane can be either passive, occurring without the input of cellular energy, or active, requiring the cell to expend energy in moving it. The membrane also maintains the cell potential.
Specific proteins embedded in the cell membrane can act as molecular signals that allow cells to communicate with each other. Protein receptors are found ubiquitously and function to receive signals from both the environment and other cells. These signals are transduced into a form that the cell can use to directly effect a response. Other proteins on the surface of the cell membrane serve as "markers" that identify a cell to other cells. The interaction of these markers with their respective receptors forms the basis of cell-cell interaction in the immune system.
Structure
Lipid bilayer
The cell membrane consists primarily of a thin layer of amphipathicphospholipids which spontaneously arrange so that the hydrophobic "tail" regions are shielded from the surrounding polar fluid, causing the more hydrophilic "head" regions to associate with the cytosolic and extracellular faces of the resulting bilayer. This forms a continuous, spherical lipid bilayer approximately 7 nm thick, barely discernible with a transmission electron microscope.[1]
The arrangement of hydrophilic and hydrophobic heads of the lipid bilayer prevent polar solutes (e.g. amino acids, nucleic acids, carbohydrates, proteins, and ions) from diffusing across the membrane, but generally allows for the passive diffusion of hydrophobic molecules. This affords the cell the ability to control the movement of these substances via transmembrane protein complexes such as pores and gates.
Flippases and Scramblases concentrate phosphatidyl serine, which carries a negative charge, on the inner membrane. Along with NANA, this creates an extra barrier to charged moities moving through the membrane.
Membranes serve diverse functions in eukaryotic and prokaryotic cells. One important role is to regulate the movement of materials into and out of cells. The phospholipid bilayer structure (fluid mosaic model) with specific membrane proteins accounts for the selective permeability of the membrane and passive and active transport mechanisms. In addition, membranes in prokaryotes and in the mitochondria and chloroplasts of eukaryotes facilitate the synthesis of ATP through chemiosmosis.
Integral membrane proteins
The cell membrane contains many integral membrane proteins, which pepper the entire surface. These structures, which can be visualized by electron microscopy or fluorescence microscopy, can be found on the inside of the membrane, the outside, or membrane spanning. These may include integrins, cadherins, desmosomes, clathrin-coated pits, caveolaes, and different structures involved in cell adhesion.
Membrane skeleton
The cytoskeleton is found underlying the cell membrane in the cytoplasm and provides a scaffolding for membrane proteins to anchor to, as well as forming organelles that extend from the cell. Anchoring proteins restricts them to a particular cell surface — for example, the apical surface of epithelial cells that line the vertebrategut — and limits how far they may diffuse within the bilayer. The cytoskeleton is able to form appendage-like organelles, such as cilia, which are microtubule-based extensions covered by the cell membrane, and filopodia, which are actin-based extensions. These extensions are ensheathed in membrane and project from the surface of the cell in order to sense the external environment and/or make contact with the substrate or other cells. The apical surfaces of epithelial cells are dense with actin-based finger-like projections known as microvilli, which increase cell surface area and thereby increase the absorption rate of nutrients. Localized decoupling of the cytoskeleton and cell membrane results in formation of a bleb.
Structure and the Fluid mosaic model
| Please help improve this article or section by expanding it. Further information might be found on the talk page or at requests for expansion. (June 2008) |
According to the fluid mosaic model of S. J. Singer and Garth Nicolson, the biological membranes can be considered as a two-dimensional liquid where all lipid and protein molecules diffuse more or less freely[2]. This picture may be valid in the space scale of 10 nm. However, the plasma membranes contain different structures or domains that can be classified as (a) protein-protein complexes; (b) lipid rafts, (c) pickets and fences formed by the actin-based cytoskeleton; and (d) large stable structures, such as synapses or desmosomes.
The fluid mosaic model can be seen when the membrane proteins of two cells (e.g., a human cell and a mouse cell) are tagged with different-coloured fluorescent labels. When the two cells are fused, the two colours intermix, indicating that the proteins are free to move in the 2D plane.
Composition
Cell membranes contain a variety of biological molecules, notable lipids and proteins. Material is incorporated into the membrane, or deleted from it, by a variety of mechanisms:
- Fusion of intracellular vesicles with the membrane (exocytosis) not only excretes the contents of the vesicle but also incorporates the vesicle membrane's components into the cell membrane. The membrane may form blebs around extracellular material that pinch off to become vesicles (endocytosis).
- If a membrane is continuous with a tubular structure made of membrane material, then material from the tube can be drawn into the membrane continuously.
- Although the concentration of membrane components in the aqueous phase is low (stable membrane components have low solubility in water), exchange of molecules with this small reservoir is possible.
In all cases, the mechanical tension in the membrane has an effect on the rate of exchange. In some cells, usually having a smooth shape, the membrane tension and area are interrelated by elastic and dynamical mechanical properties, and the time-dependent interrelation is sometimes called homeostasis, area regulation or tension regulation.
Lipids
The cell membrane consists of three classes of amphipathic lipids: phospholipids, glycolipids, and steroids. The amount of each depends upon the type of cell, but in the majority of cases phospholipids are the most abundant.[3] In RBC studies, 30% of the plasma membrane is lipid.
The fatty chains in phospholipids and glycolipids usually contain an even number of carbon atoms, typically between 14 and 24. The 16- and 18-carbon fatty acids are the most common. Fatty acids may be saturated or unsaturated, with the configuration of the double bonds nearly always cis. The length and the degree of unsaturation of fatty acids chains have a profound effect on membranes fluidity[4] as unsaturated lipids create a kink, preventing the fatty acids from packing together as tightly, thus decreasing the melting point (increasing the fluidity) of the membrane. The ability of some organisms to regulate the fluidity of their cell membranes by altering lipid composition is called homeoviscous adaptation.
The entire membrane is held together via non-covalent interaction of hydrophobic tails, however the structure is quite fluid and not fixed rigidly in place. Phospholipid molecules in the cell membrane are "fluid" in the sense that they are free to diffuse and exhibit rapid lateral diffusion along the layer in which they are present. However, movement of phospholipid molecules between layers is not energetically favourable and does not occur to an appreciable extent. Lipid rafts and caveolae are examples of cholesterol-enriched microdomains in the cell membrane.
In animal cells cholesterol is normally found dispersed in varying degrees throughout cell membranes, in the irregular spaces between the hydrophobic tails of the membrane lipids, where it confers a stiffening and strengthening effect on the membrane.[1]
Carbohydrates
About 5% of the plasma membrane weight is carbohydrate, predominantly glycoprotein, but with some lipoprotein (cerebrosides and gangliosides). For the most part, no glycosylation occurs on other unit membranes, and only ever occurs on the extracellular surface of cell membranes.
The glycocalyx is an important feature in all cells, especially epithelia with microvilli. Recent data suggest the glycocalyx participates in cell adhesion, lymphocyte homing, and many others.
The penultimate sugar is galactose and the terminal sugar is sialic acid, as the sugar backbone is modified in the golgi apparatus. Sialic acid carries a negative charge, providing an external barrier to charged particles.
Proteins
| Type | Description | Examples |
| Integral proteins or transmembrane proteins | Span the membrane and have a hydrophilic cytosolicdomain, which interacts with internal molecules, a hydrophobic membrane-spanning domain that anchors it within the cell membrane, and a hydrophilic extracellular domain that interacts with external molecules. The hydrophobic domain consists of one, multiple, or a combination of α-helices and β sheet protein motifs. | Ion channels, proton pumps, G protein-coupled receptor |
| Lipid anchored proteins | Covalently-bound to single or multiple lipid molecules; hydrophobically insert into the cell membrane and anchor the protein. The protein itself is not in contact with the membrane. | G proteins |
| Peripheral proteins | Attached to integral membrane proteins, or associated with peripheral regions of the lipid bilayer. These proteins tend to have only temporary interactions with biological membranes, and, once reacted the molecule, dissociates to carry on its work in the cytoplasm. | Some enzymes, some hormones |
The cell membrane plays host to a large amount of protein that is responsible for its various activities. The amount of protein differs between species and according to function, however the typical amount in a cell membrane is 50%.[4] These proteins are undoubtedly important to a cell: Approximately a third of the genes in yeast code specifically for them, and this number is even higher in multicellular organisms.[3]
The cell membrane, being exposed to the outside environment, is an important site of cell-cell communication. As such, a large variety of protein receptors and identification proteins, such as antigens, are present on the surface of the membrane. Functions of membrane proteins can also include cell-cell contact, surface recognition, cytoskeleton contact, signalling, enzymic activity, or transporting substances across the membrane.
Most membrane proteins must be inserted in some way into the membrane. For this to occur, an N-terminus "signal sequence" of amino acids directs proteins to the endoplasmic reticulum, which inserts the proteins into a lipid bilayer. Once inserted, the proteins is then transported to its final destination in vesicles, where the vesicle fuses with the target membrane.
Variation
The cell membrane has slightly different composition in different cell types and has therefore different denominations in different cell types:
- Sarcolemma in myocytes
- Oolemma in oocytes.
Permeability
The permeability of membranes is the ease of molecules to pass it. This depends mainly on electric charge and, to a slightly lesser extent, on the molar mass of the molecule. Electrically-neutral and small molecules pass the membrane easier than charged, large ones.
The electric charge phenomenon results in pH parturition of substances throughout the fluid compartments of the body.
Monday, August 25, 2008
DNA Replication
| DNA Replication How DNA Makes Copies of Itself |
Primers Replication occurs differently on antiparallel strands of DNA. That nucleotides can be added only to the sugar or 3' end of the growing complementary chain presents no problem for the side of the DNA chain opening at its phosphate or 5' end. The primer that binds to the first few exposed bases will end with a sugar (3') where the phosphate of a new nucleotide can be attached. From there on, DNA polymerase can continuously synthesize the growing complementary strand. This strand of DNA is called the leading strand. A nice little animation of DNA synthesis on the leading strand can be seen at the Nobel Prize e-museum site at http://www.nobel.se/medicine/educational/dna/a/replication/replication_ani.html. A different challenge faces DNA polymerase when the complementary side of the DNA molecule begins unzipping from its sugar (3') toward its phosphate (5') end. A primer of complementary molecules attaching to the opening end of this chain would have a phosphate not a sugar at its exposed end so that new nucleotides could not be joined. To get around this problem, this strand is synthesized in small pieces backward from the overall direction of replication. This strand is called the lagging strand. The short segments of newly assembled DNA from which the lagging strand is built are calledOkazaki fragments. As replication proceeds and nucleotides are added to the 3' end of the Okazaki fragments, they come to meet each other. The primer fragments are then booted out by enzymes and replaced by appropriate DNA nucleotides. The whole thing is then stitched together by another enzyme called DNA ligase. The Nobel e-museum also has an animation of this process at http://www.nobel.se/medicine/educational/dna/a/replication/lagging_ani.html .
Replication occurs simultaneously at multiple places along a DNA strand. Because human DNA is so very long (with up to 80 million base pairs in a chromosome) it unzips at multiple places along its length so that the replication process is going on simultaneously at hundreds of places along the length of the chain. Eventually these areas run together to form a complete chain. In humans, DNA is copied at about50base pairs per second. The process would take a month (rather than the hour it actually does) without these multiple places on the chromosome where replication can begin. DNA replication is extraordinarily accurate. DNA polymerase makes very few errors, and most of those that are made are quickly corrected by DNA polymerase and other enzymes that "proofread" the nucleotides added into the new DNA strand. If a newly added nucleotide is not complementary to the one on the template strand, these enzymes remove the nucleotide and replace it with the correct one. With this system, a cell's DNA iscopied with less than one mistake in a billion nucleotides. This is equal to a person copying 100 large (1000 page) dictionaries word for word, and symbol for symbol, with only one error for the whole process! |
Meiosis
Meiosis How Chromosomes are passed from parent to offspring | |||||||||
The process by which the chromosome number is halved and chromosomes are sorted and packaged to be passed on to an organism’s offspring is called meiosis. Each of the resulting reproductive cells, or gametes(sperm and egg), has only a single set of 22 autosomes plus a single sex chromosome, either an X or a Y. A cell with a single chromosome set is called a haploid cell. By means of sexual intercourse, a sperm cell carrying one 23 chromosome set from the father reaches and fuses with an egg cell carrying a corresponding set of 23 chromosomes from the mother. The resulting fertilized egg, or zygote, contains the two haploid sets of chromosomes bearing genes originating in both the maternal and paternal family lines. As a human develops from a zygote to a sexually mature adult, the new combination of genes in the zygote are passed on with precision to all somatic cells of the body by the process ofmitosis. | |||||||||
The process of meiosis has many similarities to the process of mitosis--chromosomes replicate before the process begins and shorten and thicken to look like the chromosomes at the beginning of mitosis. A spindle with fibers appears and the nuclear membrane dissolves. | |||||||||
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The chromosomes in each sperm or egg are a random mix from the maternal set and paternal set of the original cell. Because each of the 23 pairs of chromosomes can line up in two different ways one person can produce more than 8 million (223) different kinds of eggs or sperm. When fertilization occurs, 223 x 223 or 70 trillion different zygotes are possible! For the genealogist, this means that any one of his or her chromosomes could have come from any one of eight great-grandparents or, going back say twenty generations, from any one of over a million potential ancestors (in reality, many of these potential ancestors may be the same individuals as lines cross and intermarry over generations.) In the same light, after so many generations of shuffling and dividing, contributions from some ancestors may have been lost completely. With only one exception, it is impossible to trace the path of individual chromosomes in the nucleus from generation to generation. | |||||||||
Differences Between Sperm and Egg Formation What they mean to the molecular genealogist A mature sperm has a head, which contains a nucleus with its haploid set of chromosomes, a long tail which propels the sperm through its fluid surroundings, and between these a midpiece containing several hundred mitochondria which supply the energy necessary for the long journey in search of the egg. On the other hand, the development of the egg cell involves an unequal cell division. It produces one relatively large primary egg cell which receives all of the cell parts--including thousands of mitochondria--from the starting cell while the other three cells that result from the meiotic process form small polar bodies that, at first, attach themselves to the surface of the primary egg but eventually deteriorate. At fertilization, the entire sperm does not enter the egg. Practically the only contribution that the sperm cell makes to the zygote is its haploid nucleus with its set of 23 chromosomes. Importantly to the genealogist, the tail and midsection of the sperm drop off outside the egg meaning that virtually no mitochondria from the male parent enter the zygote. All of the mitochondria (with its own DNA you will recall) in the developing embryo come from the mother. The diagram below illustrates the differences between the formation of sperm and egg cells.
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The cross-over animation above is a modification of an animation by | |||||||||