Bioinformatics sequencing excercise. Sequencing the human genome sta.pdf

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Bioinformatics sequencing excercise. Sequencing the human genome started with how many base pairs? Where are all of those base pairs located? Sequencing that many base pairs was and still is not feasible. So what did scientists do to begin the international effort to sequence the genome? What two processes were used to sequence the human genome? What is the difference between the two processes? Sequencing of the genome helps to know the sequence of the genes and mapping is to identify location of genes and distance between genes on the chromosomes. Who was the director of the International Human Genome Sequencing Project? Why is this process call hierarchical clone by clone sequencing? The DNA is split up into fragments ready for sequencing. What is the Golden Tiling Path? Where does it fit into the process on the illustration of the hierarchical clone by clone sequencing process. What is the purpose of using BACs in the sequencing process? How long are the sequences carried by each BAC clone? What is un Solution 1) The Human Genome Project started in 1990 and aimed in sequencing all three billion base pairs. The genome was broken into 150,000 base pairs in length and then ligated and cloned into BAC 2) The nucleotides Adenine, Thymine, Guanine and cytosine are located in the DNA in the nucleus. Mitochondria and chloroplast also carry genetic material as plasmid hence they are self replicating. 3) The DNA was cut into fragments of 150,000 base pairs and ligated into BAC. They created a shortgun and assembled and sequenced it. 5)Francis Collins is the director of NHGRI 9) 150,000 base pairs are present in one BAC. it takes about 20,000 different BAC clones to contain the 3 billion pairs.

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1. What did researchers find when they sequenced the centromeres of Arabidopsis? Why was this finding surprising? Ans: Before the Arabidopsis sequences were obtained it was thought that these repeat sequences were by far the principal component of centromeric DNA. However, Arabidopsis centromeres also contain multiple copies of genome-wide repeats, along with a few genes, the latter at a density of 7–9 per 100 kb compared with 25 genes per 100 kb for the noncentromeric regions of Arabidopsis chromosomes. The discovery that centromeric DNA contains genes was a big surprise because it was thought that these regions were genetically inactive. 2. What differences in gene distribution and repetitive DNA content are seen when yeast and human chromosomes are compared? Ans. A typical region of a human chromosome will have few genes (most of which will contain introns), several repeated sequences, and a large amount of nonrepetitive, nongenic DNA. Yeast chromosomes have higher gene densities, with very few genes containing introns, and have few repeated sequences and much less nongenic DNA. 3. The human genome contains about 50,000 fewer genes than was predicted by many researchers. Why were these initial predictions so high? Ans. These early estimates were high because they were based on the supposition that, in most cases, a single gene specifies a single mRNA and a single protein. According to this model, the number of genes in the human genome should be similar to the number of proteins in human cells, leading to the estimates of 80,000–100,000. The discovery that the number of genes is much lower than this indicates that alternative splicing, the process by which exons from a pre-mRNA are assembled in different combinations so that more than one protein can be coded by a single gene is more prevalent than was originally appreciated. 4. What are the different methods used to catalog genes? What are the advantages or disadvantages of these methods? Ans. Gene catalogs can be based on the known functions of genes, but such catalogs are incomplete because in most genomes many genes have unknown functions. Gene catalogs that are based on the identities of protein domains coded by genes are more comprehensive as these include many genes whose specific functions are unknown. 5. What is the function of the different genes in the human globin gene families? Ans. The globins are the blood proteins that combine to make hemoglobin, each molecule of hemoglobin being made up of two a-type and two b-type globins.The a-globin cluster is located on chromosome 16 and the b-cluster on chromosome 11. Both clusters contain genes that are expressed at different developmental stages and each includes at least one pseudogene. Note that expression of the a-type gene x2 begins in the embryo and continues during the fetal stage; there is no fetal-specific a-type globin. The q pseudogene is expressed but its protein product is inactive. None of the other p

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In what ways are humans also primatesSolutionBoth humans and .pdf

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In what ways are humans also primates? Solution Both humans and primates (Pottos, lemurs) do possess vertebral column and possess finger digits for the catching prey. The primates are often locomotion on its front knuckles, which is same as primate character of locomotion in apes, gorillas and chimpanzees & humans. The behavioral aspects and hunting prey finally chewing & eating the prey are main similar aspects of primates and humans commonly Primates have enable to keep its claws followed by middle digits similar to humans that support its entire weight along with metacarpophalangeal joints and interphalangeal joints finally produces \"hook-and-pull\" digger with enlarged supraspinous fossa. This type of movement is going to enable to increase pulling power of forelimbs. The adaptations historically developed by primates are nearly similar to humans for \"homeostatic capabilities\", such as “various excretory routes & connective tissues such as blood” to eliminate nitrogenous waste etc. They have neurological innervations to these organs to mediate homeostasis similar to humans. For example, skin and sweating is often referred as an evolutionary adaptation in primates because sweat glands in humans (vertebrate animals) eliminate nitrogenous wastes such as urea, uric acid because they live in terrestrial and land environment. The development of nephrons and lungs to eliminate excess bicarbonate to keep the body with homeostasis is another major homeostatic capability. The body is going to generate heat from the liver and body hair on the humans & primates do maintain constant body temperature (negative feedback for thermoregulation) to mediate homeostasis finally to promote metabolism. Other anti-stress hormones released in gorillas body often maintain homeostasis.

i need Understand the role of capillaries in fluidnutrient exchange.pdf

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i need Understand the role of capillaries in fluid/nutrient exchange. How is blood directed to or away from particular capillary beds? Solution Capillaries are the tiniest blood vessels that are present in the body of an organism and facilitate the transition between arteries and veins. The Arteries bring the blood from the heart to the various organs of the body and the size of these vessels decreases to form arterioles and the further decreases till the time it becomes a capillary. These capillaries are small in size but more in number and thus form a network over any specific organ. these capillaries then as the blood flows further turn into broader blood vessels and eventually the veins which carry the blood back to the heart. These capillaries can be called as microscopic blood vessels as many a times they may have walls that are made of only a single celled endothelial layer. Their microscopic structure makes material exchange possible as capillaries are the only blood vessels that can carry out the fluid and nutrient exchange. Due to the presence of a large network the surface area for exchange by these capillaries is huge. The capillaries at any time hold only about 5% of the total blood volume and the human body has approximately 40 billion capillaries. the size of the capillaries is only 5–10 nm in diameter. At any given time only a around 25 percent of capillaries are fully filled with blood, especially in tissues at rest, as blood flow in microvessels is dependent on the metabolic activity of the tissue and is regulated at the sites of their origin by sphincter muscles. There are three types of capillaries based on their structures – Continuous capillaries, fenestrated capillaries and sinusoids. Continuous capillaries are found in the skin and muscles which have an uninterrupted lining of endothelial cells held together by tight junctions. Fenestrated capillaries are found wherever active capillary absorption or filtrate formation occurs like small intestine etc., having pores in the endothelium to facilitate diffusion. The Sinusoids have a slow blood flow and are modified by leaky pored capillaries with lumens for exchange of large molecules. The structurally different capillaries are present to facilitate the transport according to the functional requirement of the body. The main function of capillaries is exchange of material – Gases, nutrients and fluids. The exchange of gases is primarily of oxygen and carbon di oxide. This exchange occurs by basic diffusion through the semipermeable layers. The gases move from higher to lower concentration. In the lungs the oxygen enters the blood though the blood capillaries and the carbon di oxide is taken up at regions where oxygen is given out of the blood, in organs that have accumulated the increased carbon di oxide levels after respiration process is done. Gases can easily pass through the semi permeable layers of the capillary walls. The lipid soluble substances can also easily pass .

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In what ways are humans also primatesSolutionBoth humans and .pdf

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Give an explanation of the trait below. SolutionIt is dominant.pdf

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ecosystem ecologyTheme Physical Template of Terrestrial Environme.pdf

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ecosystem ecology Theme: Physical Template of Terrestrial Environments – Heterogeneity Discuss the physical diversity of terrestrial environments at a global scale and the abiotic factors responsible for heterogeneity at that scale Solution Terrestrial environments are generally has large heterogeneity because of habitat provided by plants which is favourable for most habitats ,plants are present in both above and below ground. Moreover, physical gradients tend to be steeper, and extremes, for instance of temperature, tend to be greater in terrestrial environments. Thus it has more habitat diversity. . The most important abiotic factors responsible for heterogeneity are temperature ranges, moisture availability, light, and nutrient availability, which together determine what types of life are most likely to flourish in specific regions and what environmental challenges they will face..

Distribution of Resources Whether a resource is distributed evenly a.pdf

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Distribution of Resources Whether a resource is distributed evenly among member, of a population is often an important political or economic question How can we measure this? How can we decide if the distribution of wealth in this country is becoming more or less equitable over time? How can we measure which country has the most equitable income distribution? This problem describes a way of making such measurements. Suppose the resource is distributed evenly. Then any 20% of the population will have 20% of the resource. Similarly, any 30% will have 30% of the resource and so on. If. however, the resource is not distributed evenly, the poorest pft of the population (in terms of this resource) will nut have of p% goods. Suppose F(x) represents the fraction of the resources owned by the poorest fraction i of the population. Thus F(0.4) = 0.1 means that the poorest 40% of the population owns 10% ol the resource. What would F be if the resource were distributed evenly? What must be true of any such F ? What must F(0) and F(1) equal? Is F increasing or decreasing? Is the graph of F concave up or concave down? Gini\'s index of inequality, G. is one way to measure how evenly the resource is distributed It is defined by G = 2 integrate 1 0 [x- F(x)] dx. Show graphically what G represents. Solution a) If the resource were distributed evenly then F(0.4)=0.4 i.e the poorest 40% of the population would have 40% of the total population b) F is increasing with increse in x but after reaching 1 it is constant. F is concave up F(0)=0 F(1)=1 c)G here represents how the values are distributed.

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Describe the mechanism of action of drugs effective against viral infections. Solution Viruses are organisms that do not possess cell walls or cell membranes. Moreover many viruses are made up of envelopes which are identical to cell membranes of humans. This is why it becomes a difficult task to target a virus through other conventional drugs. Antiviral drugs generally target the genetic material of the virus i.e. DNA or RNA. These are generally nucleoside analogs which stop synthesis of DNA or RNA by getting incorporated in the growing chain. There are some antiviral drugs which induce mutation in the viral genetic machinery thus killing the virus. Some anti viral drugs can prevent entry or exit of the virus to or from an infected cell by preventing fusion of viral envelope with cell membranes of the host cell..

During Mitosis and Meiosis, describe how and where errors might be m.pdf

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During Mitosis and Meiosis, describe how and where errors might be made then give examples of some diseases that occur because of such events. Solution Living cells divide to form new cells in order to repair worn-out or damaged tissues throughout an organism, and (in the gametes only) to enable the exchange of genetic material at the initial stage of the process of sexual reproduction. (A gamete is a mature sex cell, specifically the ovum of the female or the spermatozoon of the male.) The two types of cell division are generally called mitosis and meiosis but, strictly, these terms refer to the stages of division of the cell nucleus for somatic (non-reproductive) and reproductive cells, respectively. Mitosis Mitosis is the type of cell division by which a single cell divides in such a way as to produce two genetically identical \"daughter cells\". This is the method by which the body produces new cells for both growth and repair of aging or damaged tissues throughout the body. Meiosis Meiosis is a \"reduction division\" in which a cell divides into four \"daughter cells\" each of which has half of the number of chromosomes of the original cell. Meiosis occurs prior to the formation of sperm (in males) and ova (in females). Meiosis only occurs in the \"gametes\". Meiosis consists of two successive divisions, each of which is divided into four phases. The first meiotic division is similar to mitosis and the second meiotic division is the \"reduction\" stage. Meiosis enables the exchange of genetic material between chromosomes. Nondisjunction is the failure of homologous chromosomes or sister chromatids to separate properly during cell division (Mitosis and Meiosis). There are three forms of nondisjunctions: 1. Failure of a pair of homologous chromosomes to separate in meiosis I, 2. Failure of sister chromatids to separate during meiosis II, and 3. Failure of sister chromatids to separate during mitosis. Nondisjunction results in daughter cells with abnormal chromosome numbers (aneuploidy). The result of this error is a cell with an imbalance of chromosomes. Such a cell is said to be aneuploid. Loss of a single chromosome (2n-1), in which the daughter cell with the defect will have one chromosome missing from one of its pairs, is referred to as a monosomy. Gaining a single chromosome, in which the daughter cell with the defect will have one chromosome in addition to its pairs is referred to as a trisomy. In the event that an aneuploidic gamete is fertilized, a number of syndromes might result. Monosomy The only known survivable monosomy in humans is Turner syndrome, where the affected individual is monosomic for the X chromosome. Other monosomies are usually lethal during early fetal development. Turner syndrome (X monosomy) (45, X0) Karyotype of X monosomy (Turner syndrome): This condition is characterized by the presence of only one X chromosome and no Y chromosome. Complete loss of an entire X chromosome accounts for about half the cases of.

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Define: indirect finance, direct finance, debt, and equity. Solution Direct finance: When a firm borrows funds directly issuing securities from financial market i.e. without help of any financial institution. Direct finance can be in nature of equity or debt Indirect finance: When firm borrows funds using financial intermediaries to raise capital for the firm. Indirect finance can be in nature of equity or debt. Equity: Equity is unit or certificate which represents the ownership in the firm. The ownership is proportionate to the value of the share or equity purchased. Equity shareholders have voting rights in the firm. No fixed payment is obligated towards equity. Debt: Debt is borrowing which a firm owes to its creditors. Debt is for specific period of time. A fixed payment is obligated towards debt which is called interest or coupon..

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An object is placed 12.9 cm in front of the cornea. (The cornea is thin ans has approximately parallel sides so that the reflection that occurs as light travels from air to cornea to aqueous humor is essentially the same as though the aqueous humor were directly in contact with the air. The aqueous humor has index of refraction n = 1.34 and the radius of curvature of cornea is 7.8 mm.) (b) The image formed by the cornea serves as an object for the lens. Treat the lens as a thin lens 7 mm behind the cornea. Find the optical power of the lens necessary to form an image on the retina, 30 mm from the center of the lens. Solution len\'s maker formula 1/f = (n-1)*(1/R1 + 1/R2 ) => 1/f = (1.34 -1)*(2/7.8) => f = 11.5 mm location of image v = (12.9*1.15)/(12.9-1.15) = 1.262 cm The image at this location acts as object for the lens. Thus, the object distance for the lens is 0.7 cm- 1.262 cm= -0.562 cm => v2 = -0.562*3)/(-0.562+3) = -0.6915 cm P = 1/f = 1/0.03 = - 33.33 D.

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An archaeal contaminant is discovered in a shipment of sausages. To which of the following groups would this contaminant most likely belong? A-methanogens B-thermophiles C-hyperthermophiles D-halophiles Solution correct answer is METHANOGENS Thermophiles, Hyperthermophiles or halohiles will be contaminating, if extreme conditions of temperature or salt concentration is present. Methanogens are present in the spoilage of shipment and produce methane leading to foul smelling..

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Can someone please explain part E to me. It\'s the only one I don\'t understand. I posted the previews b/c its needed for part E but I don\'t really get it. Solution As we can see, our data set is composed of only 0, 1, 2, which are all close to each other. Thus, there are no outliers, or unusual values. Now, we see that the graph is relatively symmetric, as the peak is at the middle, and to its left and right are not very different heights. Thus, OPTION E: There are no outliers in this relatively symmetric, mound shaped distribution. [ANSWER].

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A two-way ANOVA with interaction has how many sources of variation? a. 4 b. 2 c. 3 d. 5 Solution A two-way ANOVA with interaction has how many sources of variation? Ans is 5SourceSSdfMSFMain Effect AgivenA, a-1SS / dfMS(A) / MS(W)Main Effect BgivenB, b-1SS / dfMS(B) / MS(W)Interaction EffectgivenA*B, (a-1)(b-1)SS / dfMS(A*B) / MS(W)WithingivenN - ab, ab(n-1)SS / dfTotalsum of othersN - 1, abn - 1.

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Write a function in C++ to generate an N-node random binary search tree with distinct keys 1 through N. Assume that you have available a function, randInt(lower,upper), that generates a uniform random integer in the appropriate closed interval. What is the running time of your routine? Solution / A C++ prgroam to contrcut all unique BSTs for keys from 1 to n #include #include using namespace std; // node structure struct node { int key; struct node *left, *right; }; // A utility function to create a new BST node struct node *newNode(int item) { struct node *temp = new node; temp->key = item; temp->left = temp->right = NULL; return temp; } // A utility function to do preorder traversal of BST void preorder(struct node *root) { if (root != NULL) { cout << root->key << \" \"; preorder(root->left); preorder(root->right); } } // function for constructing trees vector constructTrees(int start, int end) { vector list; /* if start > end then subtree will be empty so returning NULL in the list */ if (start > end) { list.push_back(NULL); return list; } /* iterating through all values from start to end for constructing\\ left and right subtree recursively */ for (int i = start; i <= end; i++) { /* constructing left subtree */ vector leftSubtree = constructTrees(start, i - 1); /* constructing right subtree */ vector rightSubtree = constructTrees(i + 1, end); /* now looping through all left and right subtrees and connecting them to ith root below */ for (int j = 0; j < leftSubtree.size(); j++) { struct node* left = leftSubtree[j]; for (int k = 0; k < rightSubtree.size(); k++) { struct node * right = rightSubtree[k]; struct node * node = newNode(i);// making value i as root node->left = left; // connect left subtree node->right = right; // connect right subtree list.push_back(node); // add this tree to list } } } return list; } // Driver Program to test above functions int main() { // Construct all possible BSTs vector totalTreesFrom1toN = constructTrees(1, 3); /* Printing preorder traversal of all constructed BSTs */ cout << \"Preorder traversals of all constructed BSTs are \ \"; for (int i = 0; i < totalTreesFrom1toN.size(); i++) { preorder(totalTreesFrom1toN[i]); cout << endl; } return 0; } Output:.

Write a paragraph introducing the immunology pertaining to Crohns D.pdf

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Write a paragraph introducing the immunology pertaining to Crohn\'s Disease. This should be written in a formal scientific format specific to a scientific audience. Solution Answer : Crohn\'s disease:Its a type of inflammatory bowel disease (IBD) that may affect any part of the gastrointestinal tract from mouth to anus. Signs and symptoms often include abdominal pain, (which may be bloody if inflammation is severe), fever, and weight loss. Other complications may occur outside the gastrointestinal tract and include anemia, skin rashes, arthritis, inflammation of the eye, and feeling tired. The skin rashes may be due to infections as well as pyoderma gangrenosum or erythema nodosum. Bowel obstruction also commonly occurs and those with the disease are at greater risk of bowel cancer. Crohn\'s disease contended that the characteristic intestinal inflammation resulted from a T celldriven process initiated by usually innocuous commensal bacteria or bacterial products. Crohn\'s disease has been viewed as a paradigm of a type 1 helper T cell, with raised levels of interferon and interleukin (IL2). The mucosal inflammation is theorised to be perpetuated by a failure to down regulate this immunologically activated state with a loss of normal tolerance to commensal flora. This conception has served as the guiding principle for most current and investigational agents that aim to suppress what is considered to be an inappropriate immune response, with most approaches targeting the T cell or T cell products. Crohn\'s disease is caused by a combination of environmental, immune and bacterial factors in genetically susceptible individuals. It results in a chronic inflammatory disorder, in which the body\'s immune system attacks the gastrointestinal tract possibly directed at microbial antigens, While Crohn\'s is an immune related disease, it does not appear to be an autoimmune disease (in that the immune system is not being triggered by the body itself). The exact underlying immune problem is not clear; however, it may be an immunodeficiency state. About half of the overall risk is related to genetics with more than 70 genes found to be involved. Tobacco smokers are two times more likely to develop Crohn\'s disease than nonsmokers. It also often begins aftergastroenteritis. Diagnosis is based on a number of findings including biopsy and appearance of the bowel wall, medical imaging and description of the disease. Other conditions that can present similarly include irritable bowel syndrome and Behçet\'s disease..

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Why aren\'t conjugative plasmids degraded by Restriction-Modification systems upon transfer to a recipient cell? Solution Majority of RM systems are located on bacterial chromosomes, some of them, especially those representing type II can be found in naturally occurring plasmids. This may facilitate dissemination of these genetic elements among bacteria by means of horizontal gene transfer as suggested by bioinformatic analyses.Their primary role relies on protecting bacteria against phage invasion.When present in cells, the RM systems, apart from their aforementioned diverse functions, may also modulate the flow of incoming DNA molecules.So, they can be considered as key elements that can control circulation of genetic determinants in the environment. RM systems are rare in plasmids and the host spectrum for such plasmids is rather narrow. three factors ensure stable maintenance of plasmids are: (i) sites involved in resolution of plasmid multimers, (ii) a gene coding for endonuclease, and (iii) plasmid copy number control . So,if conjugative plasmids are degraded by RM system upon transfer to areceipient cell or descendants of cells that have lost the plasmid encoding a RM system cannot survive due to a reduced pool of DNA methyltransferase molecules. Lack of sufficient protection of the genomic DNA against the action of cognate restriction endonuclease leads directly to bacterial cell death..

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