dell laptop latitude e6400 manual

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The Viruses Creative Commons License Recommended Citations Versioning Download for free at Publication and on-going maintenance of this textbook is possible due to grant support from Oregon State University Ecampus. Suggest a correction. The Viruses Creative Commons License Recommended Citations Versioning If we break the word down it translates to “the study of small life,” where the small life refers to microorganisms or microbes. But who are the microbes. And how small are they? In the cellular camp we have the bacteria, the archaea, the fungi, and the protists (a bit of a grab bag composed of algae, protozoa, slime molds, and water molds). Cellular microbes can be either unicellular, where one cell is the entire organism, or multicellular, where hundreds, thousands or even billions of cells can make up the entire organism. In the acellular camp we have the viruses and other infectious agents, such as prions and viroids. The traditional definition describes microbes as organisms or agents that are invisible to the naked eye, indicating that one needs assistance in order to see them. That assistance is typically in the form of a microscope of some type. The only problem with that definition is that there are microbes that you can see without a microscope. Not well, but you can see them. If you take a giant fungus and chop half the cells off, the remaining cells will continue to function unimpeded. Versus if you chopped half my cells off, well, that would be a problem. Multicellular microbes, even if composed of billions of cells, are relatively simple in design, usually composed of branching filaments. Because microbes are so small and there are so many around, it is important to be able to isolate the one type that you are interested in. http://paseygol.com/userfiles/bt-mg-135-manual.xml dell laptop latitude e6400 manual, dell latitude e6400 laptop user manual, notebook dell latitude e6400 manual, manual de laptop dell latitude e6400, dell laptop latitude e6400 manual, dell laptop latitude e6400 manual free, dell laptop latitude e6400 manual user, dell laptop latitude e6400 manual download, dell laptop latitude e6400 manual setup, dell laptop latitude e6400 manual troubleshooting, dell laptop latitude e6400 manual free, dell latitude e6400 laptop manual, manual for dell latitude e6400 laptop. This involves methods of sterilization, to prevent unwanted contamination, and observation, to confirm that you have fully isolated the microbe that you want to study. If you get enough cells together in one place, you can definitely see them without a microscope!) A typical virus (let us say influenza virus) has a diameter of about 100 nanometers ( nm ). There are 1000 nanometers in every micrometer, so that shows why you need a more powerful microscope to see a virus. If a typical bacterium (let us pick on E.coli again) were inflated to be the size of the Statue of Liberty, a typical virus (again, influenza virus works) would be the size of an adult human, if we keep the correct proportions. It is hard to get people to believe that their skin is covered with billions of small creatures, if you cannot show it to them. “Seeing is believing,” that is what I always say. Or someone says that. Or at least providing the proof of their discovery, both around the same time period: He made detailed drawings of his observations, publishing them in the scientific literature of the day, and is credited with publishing the first drawings of microorganisms. In 1665 he published a book by the name of Micrographia, with drawing of microbes such as fungi, as well as other organisms and cell structures. His microscopes were restricted in their resolution, or clarity, which appeared to limit what microbes he was able to observe. He constructed a simple microscope (which has a single lens), where the lens was held between two silver plates. He made detailed drawings and notes about his observations and discoveries, sending them off to the Royal Society of London, the scientific organization of that time. This invaluable record clearly indicates that he saw both bacteria and a wide variety of protists. Some microbiologists refer to van Leeuwenhoek as the “ Father of Microbiology,” because of his contributions to the field. http://www.kontrrels.ru/imgeditor/bt_paragon_510_manual.xml Currently all organisms are grouped into one of three categories or domains: Bacteria, Archaea, and Eukarya. The Three Domain Classification, first proposed by Carl Woese in the 1970s, is based on ribosomal RNA ( rRNA ) sequences and widely accepted by scientists today as the most accurate current portrayal of organism relatedness. There are some obvious similarities, since they are mostly unicellular and cells lack a nucleus or any other organelle. But they have completely different cell walls that vary markedly in composition (but notably lack peptidoglycan) and their rRNA sequences have shown that they are not closely related to the Bacteria at all. In fact, they appear to be more closely related to the eukaryotes.The eukaryotic cell type has a nucleus, as well as many organelles, such as mitochondria or endoplasmic reticulum. They are classified separately, using characteristics specific to viruses. Viruses are typically described as “ obligate intracellular parasites,” a reference to their strict requirement for a host cell in order to replicate or increase in number. These acellular entities are often agents of disease, a result of their cell invasion. Domains are the largest grouping used, followed by numerous smaller groupings, where each smaller grouping consists of organisms that share specific features in common. Each level becomes more and more restrictive as to whom can be a member. Eventually we get down to genus and species, the groupings used for formation of a scientific name. This is the binomial nomenclature devised by Carl Linnaeus in the 1750s. There are rules in science (just like in English class, where you would never refer to “mr. robert louis stevenson,” or at least not without expecting to get your paper back with red all over it). The species name, once assigned, is permanent for the organism, while the genus can change if new information becomes available. https://www.interactivelearnings.com/forum/selenium-using-c/topic/13799/3m-x55-projector-manual For example, the bacterium previously known as Streptococcus faecalis is now Enterococcus faecalis because sequencing information indicates that it is more closely related to the members of the Enterococcus genus. It is important to note that it is inappropriate to refer to an organism by the species alone (i.e. you should never refer to E. coli as “ coli ” alone. Other bacteria can have the species “ coli ” as well.) The species is always lowercase. And both the genus and the species are italicized (common if typewritten) or underlined (common if handwritten). The genus may be shortened to its starting letter, but only if the name has been referred to in the text in its entirety at least once first (the exception to this is E. coli, due to its commonality, where hardly anyone spells out the Escherichia genus anymore). What characteristics are relevant? How did they make these contributions? Where do microbes fit in? Why are they not classified in one of the three domains? What is the system of binomial nomenclature. What are the basic rules. How are bacteria named. What is a genus and species. Be able to write a bacterial name correctly. The Viruses Creative Commons License Recommended Citations Versioning Having said that though, it is also important to note that most bacteria (about 90) have a cell wall and they typically have one of two types: a gram positive cell wall or a gram negative cell wall. Developed in 1884, it’s been in use ever since. Originally, it was not known why the Gram stain allowed for such reliable separation of bacterial into two groups. Once the electron microscope was invented in the 1940s, it was found that the staining difference correlated with differences in the cell walls. Here is a website that shows the actual steps of the Gram stain. After this stain technique is applied the gram positive bacteria will stain purple, while the gram negative bacteria will stain pink. http://acktivities.com/images/brinsea-mini-eco-manual-10-egg-incubator.pdf It’s an additional layer that typically provides some strength that the cell membrane lacks, by having a semi-rigid structure. This particular substance hasn’t been found anywhere else on Earth, other than the cell walls of bacteria. But both bacterial cell wall types contain additional ingredients as well, making the bacterial cell wall a complex structure overall, particularly when compared with the cell walls of eukaryotic microbes. The cell walls of eukaryotic microbes are typically composed of a single ingredient, like the cellulose found in algal cell walls or the chitin in fungal cell walls. It also helps maintain the cell shape, which is important for how the cell will grow, reproduce, obtain nutrients, and move. It protects the cell from osmotic lysis, as the cell moves from one environment to another or transports in nutrients from its surroundings. Since water can freely move across both the cell membrane and the cell wall, the cell is at risk for an osmotic imbalance, which could put pressure on the relatively weak plasma membrane. Studies have actually shown that the internal pressure of a cell is similar to the pressure found inside a fully inflated car tire. That is a lot of pressure for the plasma membrane to withstand. The cell wall can keep out certain molecules, such as toxins, particularly for gram negative bacteria.The chains are cross-linked to one another by a tetrapeptide that extends off the NAM sugar unit, allowing a lattice-like structure to form. The four amino acids that compose the tetrapeptide are: L-alanine, D-glutamine, L-lysine or meso -diaminopimelic acid (DPA), and D-alanine. Typically only the L-isomeric form of amino acids are utilized by cells but the use of the mirror image D-amino acids provides protection from proteases that might compromise the integrity of the cell wall by attacking the peptidoglycan. http://www.northamericatalk.com/wp-content/plugins/formcraft/file-upload/server/content/files/16288ecd091204---canon-430ex11-manual.pdf In many gram positive bacteria there is a cross-bridge of five amino acids such as glycine ( peptide interbridge ) that serves to connect one tetrapeptide to another. In either case the cross-linking serves to increase the strength of the overall structure, with more strength derived from complete cross-linking, where every tetrapeptide is bound in some way to a tetrapeptide on another NAG-NAM chain. In fact, peptidoglycan can represent up to 90 of the cell wall, with layer after layer forming around the cell membrane. The NAM tetrapeptides are typically cross-linked with a peptide interbridge and complete cross-linking is common. All of this combines together to create an incredibly strong cell wall. Teichoic acid is believed to play several important roles for the cell, such as generation of the net negative charge of the cell, which is essential for development of a proton motive force. Teichoic acid contributes to the overall rigidity of the cell wall, which is important for the maintenance of the cell shape, particularly in rod-shaped organisms. There is also evidence that teichoic acids participate in cell division, by interacting with the peptidoglycan biosynthesis machinery. Lastly, teichoic acids appear to play a role in resistance to adverse conditions such as high temperatures and high salt concentrations, as well as to ?-lactam antibiotics. Teichoic acids can either be covalently linked to peptidoglycan ( wall teichoic acids or WTA ) or connected to the cell membrane via a lipid anchor, in which case it is referred to as lipoteichoic acid. But some nutrients are too large, requiring the cell to rely on the use of exoenzymes. These extracellular enzymes are made within the cell’s cytoplasm and then secreted past the cell membrane, through the cell wall, where they function outside of the cell to break down large macromolecules into smaller components. BARSUGO.COM/ckfinder/userfiles/files/carl-zeiss-jena-service-manual.pdf They do contain peptidoglycan as well, although only a couple of layers, representing 5-10 of the total cell wall. What is most notable about the gram negative cell wall is the presence of a plasma membrane located outside of the peptidoglycan layers, known as the outer membrane. This makes up the bulk of the gram negative cell wall. The outer membrane is composed of a lipid bilayer, very similar in composition to the cell membrane with polar heads, fatty acid tails, and integral proteins. It differs from the cell membrane by the presence of large molecules known as lipopolysaccharide (LPS), which are anchored into the outer membrane and project from the cell into the environment. LPS is made up of three different components: 1) the O-antigen or O-polysaccharide, which represents the outermost part of the structure, 2) the core polysaccharide, and 3) lipid A, which anchors the LPS into the outer membrane. LPS is known to serve many different functions for the cell, such as contributing to the net negative charge for the cell, helping to stabilize the outer membrane, and providing protection from certain chemical substances by physically blocking access to other parts of the cell wall. In addition, LPS plays a role in the host response to pathogenic gram negative bacteria. The O-antigen triggers an immune response in an infected host, causing the generation of antibodies specific to that part of LPS (think of E. coli O 157). Lipid A acts as a toxin, specifically an endotoxin, causing general symptoms of illness such as fever and diarrhea. A large amount of lipid A released into the bloodstream can trigger endotoxic shock, a body-wide inflammatory response which can be life-threatening. While there are certain molecules it would like to keep out, such as antibiotics and toxic chemicals, there are nutrients that it would like to let in and the additional lipid bilayer presents a formidable barrier. https://www.saenger-ohg.de/wp-content/plugins/formcraft/file-upload/server/content/files/16288ecdfb758c---Canon-450d-manual-sensor-cleaning.pdf Large molecules are broken down by enzymes, in order to allow them to get past the LPS. Instead of exoenzymes (like the gram positive bacteria), the gram negative bacteria utilize periplasmic enzymes that are stored in the periplasm. Where is the periplasm, you ask. It is the space located between the outer surface of the cell membrane and the inner surface of the outer membrane, and it contains the gram negative peptidoglycan. Once the periplasmic enzymes have broken nutrients down to smaller molecules that can get past the LPS, they still need to be transported across the outer membrane, specifically the lipid bilayer. Gram negative cells utilize porins, which are transmembrane proteins composed of a trimer of three subunits, which form a pore across the membrane. Some porins are non-specific and transport any molecule that fits, while some porins are specific and only transport substances that they recognize by use of a binding site. Once across the outer membrane and in the periplasm, molecules work their way through the porous peptidoglycan layers before being transported by integral proteins across the cell membrane. This linkage between the two layers provides additional structural integrity and strength. Bacteria belonging to the phylum Chlamydiae appear to lack peptidoglycan, although their cell walls have a gram negative structure in all other regards (i.e. outer membrane, LPS, porin, etc). It has been suggested that they might be using a protein layer that functions in much the same way as peptidoglycan. This has an advantage to the cell in providing resistance to ?-lactam antibiotics (such as penicillin), which attack peptidoglycan. They often strengthen their cell membrane somewhat by the addition of sterols, a substance usually associated with eukaryotic cell membranes. Many members of this phylum are pathogens, choosing to hide out within the protective environment of a host. What components are present and how do they interact. http://www.zav-mito.si/wp-content/plugins/formcraft/file-upload/server/content/files/16288ece3a8219---canon-450d-manual-lens.pdf Be able to diagram peptidoglycan and its’ components. What different types of cross-linking are there? What are lipteichoic acids? What purpose can it serve. What alternatives are available for cells? How is it linked to the cell. What is a porin and what are their functions? What advantage does this confer. The Viruses Creative Commons License Recommended Citations Versioning Yeah, well, size isn’t everything. But numbers, that is something. Be sure to pay careful attention to the microbes in between!) Not Ghostbusters TM, that’s for sure. I would try someone with a microscope. (Microscope Man? Maybe not.) Now I will admit, with the advent of molecular biology there’s a lot of microbiology nowadays that happens without a microscope. And, since “seeing is believing,” it was the visualization of microbes that got people interested in them in the first place. His illustrations and observations from a variety of objects viewed under a microscope were published in the book Micrographia. Hooke used a compound microscope, meaning it contained two sets of lenses for magnification: the ocular lens next to the eye and the objective lens, next to the specimen or object. The magnification of a compound microscope is a product of the ocular lens magnification and the objective lens magnification. Thus a microscope with an ocular magnification of 10x and an objective magnification of 50x would have a total magnification of 500x. You can see a drawing of Hooke’s microscope. He was a cloth merchant from Holland who was believed to be inspired by Mr. Hooke’s work, probably with the original intention of examining textiles to determine quality. Very quickly van Leeuwenhoek started examining just about everything under the microscope and we know this because he kept detailed notes about both his samples and his observations. Van Leeuwenhoek was using what is called a simple microscope, a microscope with just a single lens. Essentially, it is a magnifying glass. chongthamhaiphong.com/upload/files/carl-zeiss-iol-master-user-manual.pdf But the lenses that he produced were of such high quality that he is given credit for the discovery of single-celled life forms. You can learn more about van Leeuwenhoek’s observations. If you want to understand the limitations of a light microscope you have to understand concepts like resolution, wavelength, and numerical aperture, where their relationship to one another is summed up by the Abbe equation: So, in the Abbe equation d becomes the minimal distance where two objects next to one another can be resolved or distinguished as individual objects. Resolution is dependent upon the wavelength of illumination being used, where a shorter wavelength will result in a smaller d. Lastly, we have the effect of the numerical aperture, which is a function of the objective lens and its ability to gather light. The numerical aperture value is actually defined by two components: n, which is the refractive index of the medium the lens is working in, and sin ?, which is a measurement of the cone of light that enters the objective. A lens can typically work in two media: air, with a refractive index of 1.00, or oil, with a refractive index of 1.25. Oil will allow more of the light to be collected, by directing more of the light rays into the objective lens. The maximum total magnification for a microscope using visual light for illumination is around 1500X, where the microscope might have 15x oculars and a 100x oil immersion objective. The highest resolution possible is around 0.2 ?m. If objects or cells are closer together than this, they can’t be distinguished as separate entities. And then there are so many microscopes, so little time. The type that you need depends upon the specific type of microbes that you want to visualize. Let us look at the details of each type: Here is a website on the basic parts of a bright-field compound microscope, in case you are not enrolled in the general microbiology lab. The specimen is illuminated by a light source at the base of the microscope and then initially magnified by the objective lens, before being magnified again by the ocular lens. Remember that the total magnification achieved is a product of the magnification of both lenses. But that does not apply to unstained bacteria, which have very little contrast with their environment, unless the cells are naturally pigmented. That is why staining (see section below) is such an important concept in microscopy. A bright-field microscope will work reasonably well to view the larger eukaryotic microbes (i.e. protozoa, algae) without stain, but unstained bacteria will be almost invisible. Stained bacteria will appear dark against a bright background (ah, I knew that there was a reason for the term “bright-field.”) In fact, you could make this modification to the microscope you have at home. It makes use of what is known as a dark-field stop, an opaque disk that blocks light directly underneath the specimen so that light reaches it from the sides. The result is that only light that has been reflected or refracted by the specimen will be collected by the objective lens, resulting in cells that appear bright against a dark background (thus the term “dark-field.” Yes, it’s all making sense now). This allows for observation of living, unstained cells which is particularly nice if you want to observe motility or eukaryotic organelles. This microscope also uses an opaque ring or annular stop, but this one has a transparent ring that only releases light in a hollow cone. The principle of this microscope gets back to the idea of refractive index and the fact that cells have a different refractive index than their surroundings, resulting in light that differs slightly in phase. The difference is amplified by a phase ring found in a special phase objective. The phase differences can be translated into differences in brightness, resulting in a dark image amidst a bright background. This allows for the observation of living, unstained cells, once again useful to observe motility or eukaryotic organelles. But it uses polarized light that is then split into two beams by a prism. One beam of light passes through the specimen, the other passes through the surrounding area. When the beams are combined via a second prism they “interfere” with one another, due to being out of phase. The resulting images have an almost 3D effect, useful for observing living, unstained cells. A mercury-arc lamp is used to generate an intense beam of light that is filtered to produce a specific wavelength of light directed at the specimen by use of dichromatic mirror, which reflects short wavelengths and transmits longer wavelengths. Naturally fluorescent organisms will absorb the short-wavelengths and emit fluorescent light with a longer wavelength that will pass through the dichromatic mirror and can be visualized. There are a variety of microbes with natural fluorescence but there are certainly far more organisms that lack this quality. Visualization of the latter organisms depends upon the use of fluorochromes, fluorescent dyes that bind to specific cell components. The fluorochromes can also be attached to antibodies, to highlight specific structures or areas of the cell, or even different organisms. A CSLM uses a laser for illumination, due to the high intensity. The light is directed at dichromatic mirrors that move, “scanning” the specimen. The longer wavelengths emitted by the fluorescently stained specimen pass back through the mirrors, through a pinhole, and are measured by a detector. The pinhole serves to con jugate the focal point of the lens (ah, that’s where the term confocal came from!), which means it allows for complete focus of a given point. Since the entire specimen is scanned in the x-z planes (all three axes), the information acquired by the detector can be compiled by a computer to create a single 3D image entirely in focus. This is a particularly useful tool for viewing complex structures such as biofilms. It helps to make something so small a bit easier to see, by providing contrast between the microorganism and its background. A simple stain makes use of a single dye, either to stain the cells directly ( direct stain ) or to stain the background surrounding the cells ( negative stain ). From this a researcher can gather basic information about a cell’s size, morphology (shape), and cell arrangement. The Gram stain, developed in 1884, is the most common differential stain used in microbiology, where bacterial cells are separated based on their cell wall type: gram positive bacteria which stain purple and gram negative bacteria which stain pink. Some bacteria have a specialized cell wall that must be stained with the acid-fast stain, where acid-fast bacteria stain red and non-acid-fast bacteria stain blue. Other differential stains target specific bacterial structures, such as endospores, capsules, and flagella, to be talked about later. Remember that the limit of resolution for a light microscope is 0.2 ?m or 200 nm and most viruses are smaller than that. So, we need something more powerful. Enter the electron microscopes, which replace light with electrons for visualization. Since electrons have a wavelength of 1.23 nm (as opposed to the 530 nm wavelength of blue-green light), resolution increases to around 0.5 nm, with magnifications over 150,000x. The drawback of using electrons is that they must be contained in a vacuum, eliminating the possibility of working with live cells. There is also some concern that the extensive sample preparation might distort the specimen’s characteristics or cause artifacts to form. Dense areas scatter the electrons, resulting in a dark area on the image, while electrons can pass (or “transmit”) through the less dense areas, resulting in a brighter section. The image is generated on a fluorescent screen and can then be captured. The resulting pictures represent one slice or plane of the specimen. More electrons are released from raised areas of the specimen, while less secondary electrons will be collected from sunken areas. In addition, the electron beam is scanned over the specimen surface, producing a 3D image of the external features. Most have been colorized, but they are quite stunning. On the other end of the spectrum, here are pictures taken with the Intel Play QX3, a plastic microscope for children. Be careful, you could get lost in this website. But it is great to see what an inexpensive microscope can produce in the hands of someone who knows what they’re doing. These pictures are stunning as well. These microscopes can be used in microbiology but more often they are used in other fields, to allow visualization of chemicals, metals, magnetic samples, and nanoparticles, wherever the 0.1 nm resolution and 100,000,000x magnification might be needed. Resolution is so high because the probe size is much smaller than the wavelength of either visible light or electrons. Both microscopes can be used to study objects in liquid, allowing for the examination of biological molecules. There are two different types of scanning probe microscopes, the scanning tunneling microscope (STM) and the atomic force microscope (AFM): This tunneling current is maintained by raising and lowering the probe to sustain a constant height above the sample. The resulting motion is tracked by a computer, which generates the final image. The microscope utilizes a cantilever with an extremely sharp probe tip that maintains a constant height above the specimen, typically by direct contact with the sample. Movement of the cantilever to maintain this contact deflects a laser beam, translating into an image of the object. Once again, computers are used to generate the image. How did their contributions differ. How is total magnification determined? What components impact resolution. What is the function of immersion oil? How does it improve resolution compared to other light microscopes? What are the general categories of stains and how are they used? What are the effective magnification, resolution and main uses of electron microscopes? Why are they useful for studying biological molecules. What is the difference in the scanning tunneling and the atomic force microscope? What are the limitations of microscopes and the information that we get from them. The Viruses Creative Commons License Recommended Citations Versioning More reliable genetic analysis revealed that the Archaea are distinct from both Bacteria and Eukaryotes, earning them their own domain in the Three Domain Classification originally proposed by Woese in 1977, alongside the Eukarya and the Bacteria. Perhaps most importantly, they lack a nucleus or other membrane-bound organelles, putting them into the prokaryotic category (if you are using the traditional classification scheme). Most of them are unicellular, they have 70S sized ribosomes, they are typically a few micrometers in size, and they reproduce asexually only. They are known to have many of the same structures that bacteria can have, such as plasmids, inclusions, flagella, and pili. Capsules and slime layers have been found but appear to be rare in archaea. One such characteristic is chirality of the glycerol linkage between the phopholipid head and the side chain. In archaea it is in the L-isomeric form, while bacteria and eukaryotes have the D-isomeric form. A second difference is the presence of an ether-linkage between the glycerol and the side chain, as opposed to the ester-linked lipids found in bacteria and eukaryotes. The ether-linkage provides more chemical stability to the membrane. A third and fourth difference are associated with the side chains themselves, unbranched fatty acids in bacteria and eukaryotes, while isoprenoid chains are found in archaea. These isoprenoid chains can have branching side chains.