Lecture I Cardiovascular System

Lecture I 
Cardiovascular System
HeartThe heart (Latin cor) is a hollow, muscular organ that pumps blood through the blood vessels by repeated, rhythmic contractions. The term cardiac means "related to the heart", from the Greek kardia for "heart".


 
StructureIn the human body, the heart is normally situated slightly to the left of the middle of the thorax, underneath the sternum (breastbone). It is enclosed by a sac known as the pericardium and is surrounded by the lungs. In normal adults, its mass is 250-350 g, but extremely diseased hearts can be up to 1000 g in mass. It consists of four chambers, the two upper atria (singular: atrium) and the two lower ventricles.


 
A septum divides the right atrium and ventricle from the left atrium and ventricle, preventing blood from passing between them. Valves between the atria and ventricles (atrioventricular valves) maintain coordinated unidirectional flow of blood from the atria to the ventricles.
The function of the right side of the heart (see right heart) is to collect deoxygenated blood from the body and pump it into the lungs so that carbon dioxide can be dropped off and oxygen picked up. This happens through a process called diffusion. The left side (see left heart) collects oxygenated blood from the lungs and pumps it out to the body. On both sides, the lower ventricles are thicker than the upper atria.
Oxygen-depleted or deoxygenated blood from the body enters the right atrium through two great veins, the superior vena cava, which drains the upper part of the body and the inferior vena cava that drains the lower part. The blood then passes through the tricuspid valve to the right ventricle. The right ventricle pumps the deoxygenated blood to the lungs, through the pulmonary artery. In the lungs gaseous exchange takes places and the blood releases carbon dioxide into the lung cavity and picks up oxygen. The oxygenated blood then flows through pulmonary veins to the left atrium. From the left atrium this newly oxygenated blood passes through the mitral valve to enter the left ventricle. The left ventricle then pumps the blood through the aorta to the entire body. Even the lungs take some of the blood supply from the aorta via bronchial arteries.
The left ventricle is much more muscular (1.3 - 1.5 cm thick) than the right (0.3 - 0.5 cm thick) as it has to pump blood around the entire body, which involves exerting a considerable force to overcome the vascular pressure. As the right ventricle needs to pump blood only to the lungs, it requires less muscle.
Even though the ventricles lie below the atria, the two vessels through which the blood exits the heart (the pulmonary artery and the aorta) leave the heart at its top side.
The contractile nature of the heart is due to the presence of cardiac muscle in its wall, which can work continuously without fatigue. The heart wall is made of three distinct layers. The first is the outer epicardium, which is composed of a layer of flattened epithelial cells and connective tissue. Beneath this is a much thicker myocardium made up of cardiac muscle. The endocardium is a further layer of flattened epithelial cells and connective tissue which lines the chambers of the heart.
The blood supply to the heart itself is supplied by the left and right coronary arteries, which branch off from the aorta.
The cardiac cycleThe function of the heart is to pump blood around the body. Every single beat of the heart involves a sequence of events known as the cardiac cycle, which consists of three major stages: atrial systole, ventricular systole and complete cardiac diastole. The atrial systole consists of the contraction of the atria and the corresponding influx of blood into the ventricles. Once the blood has fully left the atria, the atrioventricular valves, which are situated between the atria and ventricular chambers, close. This prevents any backflow into the atria. It is the closing of the valves that produces the familiar beating sounds of the heart, commonly referred to as the "lub-dub" sound.
 

 

The ventricular systole consists of the contraction of the ventricles and flow of blood into the circulatory system. Again, once all the blood empties from the ventricles, the pulmonary and aortic semilunar valves close. Finally complete cardiac diastole involves relaxation of the atria and ventricles in preparation for refilling with circulating blood.
Regulation of the cardiac cycleCardiac muscle is self-exciting. This is in contrast with skeletal muscle, which requires either conscious or reflex nervous stimuli. The heart's rhythmic contractions occur spontaneously, although the frequency or heart rate can be changed by nervous or hormonal influences such as exercise or the perception of danger.
The rhythmic sequence of contractions is coordinated by the sinoatrial and atrioventricular nodes. The sinoatrial node, often known as the cardiac pacemaker, is located in the upper wall of the right atrium and is responsible for the wave of electrical stimulation (See action potential) that initiates atria contraction. Once the wave reaches the atrioventricular node, situated in the lower right atrium, it is conducted through the bundles of His and causes contraction of the ventricles. The time taken for the wave to reach this node from the sinoatrial nerve creates a delay between contraction of the two chambers and ensures that each contraction is coordinated simultaneously throughout all of the heart. In the event of severe pathology, the Purkinje fibers can also act as a pacemaker; this is usually not the case because their rate of spontaneous firing is considerably lower than that of the other pacemakers and hence is overridden.
Other physiological functionsThe heart also secretes ANF (atrial natriuretic factor), a powerful peptide hormone, that affects the blood vessels, the adrenal glands, the kidneys and the regulatory regions of the brain to regulate blood pressure and volume.
Diseases and treatmentsThe study of diseases of the heart is known as cardiology. Important diseases of the heart include:
Coronary heart disease is the lack of oxygen supply to the heart muscle; it can cause severe pain and discomfort known as Angina. A heart attack occurs when heart muscle cells die because blood circulation to a part of the heart is interrupted. Congestive heart failure is the gradual loss of pumping power of the heart. Endocarditis and myocarditis are inflammations of the heart. Cardiac arrhythmia is an irregularity in the heartbeat. It is sometimes treated by implanting an artificial pacemaker Congenital heart defects. If a coronary artery is blocked or narrowed, the problem spot can be bypassed with coronary artery bypass surgery or it can be widened with angioplasty.
Beta-blockers are drugs that lower the heart rate and blood pressure and reduce the heart's oxygen requirements. Nitroglycerin and other compounds that give off nitric oxide are used to treat heart disease as they cause the dilation of coronary vessels.
All text of this article available under the terms of the GNU Free Documentation License (see Copyrights for details).

BACT MORPHOLOGY

Bacteria are unicellular microorganisms having a variety of characteristics allowing their classification. One major classification scheme is based upon their staining properties using the "Gram stain" procedure. In this procedure, heat-killed bacteria are exposed to the purple dye crystal violet and iodine. This combination forms a dye complex in the bacterial cell wall. Treatment of the stained bacteria with a decolorizer like ethanol will wash away the dye complex from some bacteria but not others. Bacteria that retain the crystal violet-iodine complex appear purple and are called "Gram-positive". Bacteria that lose the dye complex can be counterstained with the red dye saffranin so that they appear red. These bacteria are called "Gram-negative". The basis of the Gram reaction lies within the structure of the cell wall, described below. Bacteria also come in many different shapes. Spherical shapes are referred to as "cocci" while elongated cylinders are called "bacilli" or "rods". Some bacteria are slightly elongated cocci and these are referred to as "coccobacilli". Even other bacteria have a corkscrew-like appearance; these spiral forms are often called "spirochetes". Individual cells may also be arranged in pairs or clusters or chains. Thus, may morphologies are possible and these can be useful for the identification of bacterial genera. (Click here to see a bacterial classification flowchart). The ability of a bacterium to cause disease is known as its virulence. Factors involved in determining virulence potential are discussed here. In terms of the medical aspects of bacterial structure, we are most interested in those features that interact with the host. These features are found predominantly on the outer surface of the bacterial cell. This page will describe some of these features. 
SURFACE APPENDAGES Bacteria may or may not possess surface appendages that provide the organism with the ability to be motile or to transfer genetic material or to attach to host tissues. These appendages are outlined below: Flagella: These are the organs of motility. Flagella are composed of flagellins (proteins) that make up the long filament. This filament is connected to a hook and rings that anchor the flagella in the cell wall. In Gram-positive bacteria, there are two rings attached to the cytoplasmic membrane; in Gram-negative cells, an additional two rings are found in the outer membrane. Flagella may be up to 20 µm in length. Some bacteria possess a single polar flagellum (monotrichous), others have several polar flagella (lophotrichous), others have several flagella at each end of the cell (amphitrichous), and still others have many flagella covering the entire cell surface (peritrichious). Counterclockwise rotation of the flagella produces motility in a forward motion; clockwise rotation produces a tumbling motion. Flagella may serve as antigenic determinants (e.g. the H antigens of Gram-negative enteric bacteria). Pili: These surface appendages come in two distinct forms having distinct purposes. Pili (or fimbrae) may also provide antigenic determinants (e.g. the M protein of S. pyogenes). 1. Sex pili: This form of pilus can be relatively long but is often found in few numbers, generally 1 to 6, protruding from the cell surface. These structures are involved in conjugation, the transfer of genetic information from one cell to another. These structures can also provide the receptor for certain male-specific bacteriophages. 2. Common pili: This form of pilus is usually relatively short and many (about 200) and can be found covering the cell surface. These structures provide the means for attachment to host cells (e.g. epithelial cells) and often play an important role in colonization (e.g. N. gonorrhoeae). 
SURFACE LAYERS Bacteria possess several distinct surface layers that can enhance their pathogenicity. These layers are outlined below: Capsules: This type of surface layer is composed primary of high molecular weight polysaccharides. If the layer is strongly adhered to the cell wall, it is called a capsule; if not, it is called a slime layer. These layers provide resistance to phagocytosis and serve as antigenic determinants. The production of capsules is genetically and phenotypically controlled.  

BACT and ALGAE

ARCHAEBACTERIAThere are three types of archaebacteria, the most ancient of all living things. The thermoacidophiles live in the extremely hot, acidic water and moist areas within and surrounding sulfur hot springs. So closely adapted are they to their bubbly environment that they die of cold at temperatures of 55oC (131oF)!Methanogens are obligate anaerobes (free oxygen kills them) which oxidize CO2 during cellular respiration to produce methane (CH4) as a waste product. Although RNA sequencing suggests that all ten known species are evolutionarily related, they exist in environments as diverse as scalding volcanic deep-sea vents and the intestines of mammals. The reason you can light a puff of flatulence (should you choose to go into show business) is because of the symbiotic methanogens inside your guts. Strict halophiles live in extremely salty solutions such as the Dead Sea, the Great Salt Lake and that can of pickled herring you left open in the cupboard. Their pink carotenoid pigments make them conspicuous when the bacteria are present in large concentrations, as they are on the shores of some salty, land-locked lakes.
EUBACTERIAThe "true bacteria" are classified on the basis of several characteristics, of which perhaps the most familiar is the Gram Stain method.·  Gram negative EubacteriaAbout 75% of known eubacteria are gram negative. They include the gliding bacteria, the spirochetes, the curved (vibrios) and spiral (spirillae) bacteria, gram-negative rods, gram-negative cocci, rickettsias, chlamydias and the photosynthetic cyanobacteria. Gram negative bacteria form an extremely diverse group. The fact that they are all gram-negative does not necessarily imply that they comprise a monophyletic taxon. ·  Gram positive EubacteriaNot as diverse as the gram-negative bacteria, the gram-positives still make up an impressively varied group. This division includes the gram-positive rods, gram-positive cocci, and the actinomycetes, which exhibit superficial similarity and function (but no evolutionary relationship) to the (eukaryotic) fungi. 
MYCOPLASMASThese are the smallest living cells ever discovered, and are believed to have the minimum amount of DNA needed to code for a functioning cell. They lack the cell wall characteristic of the other three types of bacteria. Most mycoplasmas exist as intracellular plant or animal parasites, a life history which protects them from environmental osmotic stresses as long as the host cell is functioning properly. Penicillin, an antibiotic lethal to most other bacteria because it interferes will cell wall formation, is not effective against the naked little mycoplasmas. 

The Many Shapes of Bacteria
As you already know, bacteria come in a vast array of shapes and sizes, and there are several taxonomically distinct groups. Take a slide to your station and observe under the compound microscope. Remember: bacteria are extremely small. Focus with extreme care, on low power first, and don't break the slide! For many years, the evolutionary relationships of bacteria were so poorly understood that they were classified only on the basis of their shape and staining characteristics. These characters can still be useful in the early stages of identification, but more recent advances in DNA and RNA sequencing give us a more accurate idea of origins and relationships among these tiny, vital organisms. Each of these slides has three separate smears, each with a different shape of bacteria. Rod-shaped bacilli (sing., bacillus) are the most common. Escherichia coli (our mammalian gut symbiont), Lactobacillus spp. (which may be agents of tooth decay or ingredients in yogurt) and Bacillus anthracis (a pathogen causing anthrax in sheep and humans) are examples.Spherical cocci (sing., coccus) are also common. Streptococcus spp. are chain-forming cocci responsible for ailments such as strep throat in humans. Staphylococcus spp. form clusters reminiscent of tiny bunches of grapes (staphylo is Greek for "cluster"), and are responsible for those nasty "staph" infections (and often, gangrene) found in untreated puncture wounds.Spiral-shaped spirilla (sing., spirillum) are the largest of these three types, and the simplest to identify. Maybe you should start with those. . . 
Asexual Reproduction in ProkaryotesYou are probably most familiar with mitosis as the mode by which cells reproduce themselves. Because prokaryotes have a single, circular chromosome rather than the sets of chromosomes found in the more familiar eukaryotes, mitosis does not occur in prokaryotes. Instead, most replicate via a process of binary fission. 
Bacterial LocomotionBacteria exhibit various modes of locomotion, including "squirming", gliding and propulsion via flagella. The flagellum of a bacterium is quite different from the flagellum of a eukaryote. It is composed of a protein called flagellin, not found in eukaryotes, whereas the eukaryotic flagellum is composed of a symmetrically arranged series of microtubules. Unlike the eukaryotic flagellum, which beats with a wavelike motion, the bacterial flagellum rotates to propel the little beastie through its substrate.Here are a few images of bacterial flagella...
 Close up of the flagellum of Spirilla volutans  The spectacular Proteus vulgaris, a ubiquitous and non-pathogenic bacterium. 
The Economic Importance of Bacteria
 Bacteria affect the lives of your average Homo sapiens in countless ways. They may be pathogens, such as these Clostridium tetani. These bacilli are the pathogens responsible for causing tetanus in humans. 
 Other organisms may serve as vectors to spread bacteria. Flies, cockroaches, biting insects, rodents and other animals get a lot of the blame for transmitting diseases to humans. But if the truth be told, you're in a lot more danger of contracting somethign dangerous from personal contact with your fellow Homo sapiens than you are from being licked by a fly (or your dog!). 
 Nitrogen-fixing bacteria (such as these Rhizobiumsp.) inhabit the root cells of plants in the legume family (Fabaceae). These moneran symbionts convert gaseous nitrogen from the atmosphere (N2) into usable "fixed" nitrogen (ammonia, nitrite and nitrate) which can be absorbed by the roots and used by the plant to manufacture protein and nucleic acids. 
 Other bacteria, such as these Streptomyces spp., are sources of life-saving medicines. This genus yields the powerful antibiotic known as streptomycin. Actinomycetes are the source of actinomycin. 
 
  What are algae?     The term 'algae' is used for some lower plants and many, often unrelated groups of microorganisms that are able to perform photosynthesis.Photosynthesis (converting light energy into chemical energy) is performed in parts of the cell called chloroplasts. They can be found in different shapes and colours and in many different organisms. Not all these organisms are green. Diatoms, Chrysophytes and dinoflagellates have yellow to brown chloroplasts. There are brown algae (Phaeophyta), red algae (Rhodophyta) and many other groups of unicellular algae in many shades of green. The blue green Cyanobacteria also photosynthesize.    A very diverse groups of freshwater algae are the Chlorophytes or Green algae. Based on the compounds of the photosynthetic pigments and several other characteristics they seem closest related to plants.A common green algae is Hydrodictyon, the water net. It is a related to Pediastrum (top image) But it forms a bag-shaped colony. Like Pediastrum each individual cell can develop into a new colony. You can imagine that since the colony contains thousands of cells Hydrodictyon can reproduce very rapidly. And unlike Pediastrum, Hydrodictyon can grow large, almost 30 cm. in length. Blooms of Hydrodictyon can be a real problem for water treatment plants.The image shows a part of a small colony (left) and three individual cells of a big colony. Inside each of these cells a new colony can be formed.  

Analysis of accessible surface of residues in proteins

Analysis of accessible surface of residues in proteins

Understanding the folding of proteins remains one of the major scientific challenges. One way to explore this complex problem is to get information from the protein structures themselves. We recently developed an analytical tool, named Pex files, in which numerical data on various structural parameters of proteins are described, such as secondary structures, side chain interactions, H-bonds, and more (Thomas et al. 2001, 2002a,b). Here we introduce a new Pex file that, in addition to the major structural parameters of proteins, lists a series of parameters describing the solvent accessibility. The folding process of soluble proteins decreases the surface in contact with the solvent. This is related to the secondary structures of proteins. Accurate knowledge of residue accessibility would thus aid the prediction of secondary structures. Different methods of prediction are based on the use of protein structure databases and on multiple sequence alignments. They have various efficiencies, notably depending on the number of relative accessibility states (i.e., exposed, buried, and in-between; Rost and Sander 1994; Rost 1996; Li and Pan 2001; Naderi-Manesh et al. 2001; Yuan et al. 2002). Further, because active sites of proteins are often located at the surface of the protein, greater insight into residue accessibility would be important in understanding and predicting structure/function relationships

regulatory sequence

A rgulatory sequence (also called regulatory region or ~ element) is a promoter, enhancer or other segment of DNA where regulatory proteins such as transcription factors bind preferentially. They control gene expression and thus protein expression.

Regulatory sequences or elements can also be found in messenger RNA, but they are generally not as well studied as those in DNA. They may be bound by RNA-binding proteins or RNAs (eg miRNAs)

dna

A DNA microarray (also commonly known as gene or genome chip, DNA chip, or gene array) is a collection of microscopic DNA spots attached to a solid surface, such as glass, plastic or silicon chip forming an array for the purpose of expression profiling, monitoring expression levels for thousands of genes simultaneously.

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. Measuring gene expression using microarrays is relevant to many areas of biology and medicine, such as studying treatments, disease, and developmental stages. For example, microarrays can be used to identify disease genes by comparing gene expression in diseased and normal cells

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