MEDICINE AND SURGERY "F" Course of LABORATORY MEDICINE Disturbances of the urea cycle and ammonia detoxification METABOLISM OF AMMONIA: THE UREA CYCLE THE REGISTRATION OF ATTENDANCE TO THIS ON-LINE LECTURE IS ACTIVE!       To register your attendance please type in your surname and matricola number. Surname: Matricola: Notice that your attendance will be registered only if you completed the reading, questions, and audios, and that you cannot interrupt and resume the session (but you can repeat it as many times as you like). Remember to press the [send] button before leaving this page! A confirmation message will appear at the end of this page.       A comment section has been added at the end of this lecture. Adding a comment or question does not require registration with your matricola number, feel free to comment whenever you like.       Proteins ingested with the diet are digested to aminoacids by endopeptidases (e.g. pepsin, trypsin and chymotrypsin) and by exopeptidases (carboxypeptidases and aminopeptidases) and absorbed by the small intestine. They constitute the major source of nitrogen in our metabolism. Endogenous proteins are degraded to aminoacids by several systems (e.g. the proteasome, and the lysosomes); these may be used to produce new proteins or can be directed to the Krebs cycle to produce energy.       Since the Krebs cycle does not consume nitrogen, the catabolism of aminoacids requires the removal of the amino group. This is achieved by enzymes called transaminases (or aminotransferases). There are as many transaminases as there are aminoacids, and each uses α-ketoglutaric acid (a metabolyte of the Krebs cycle) as the acceptor of the amino group; the reaction of Alanine Aminotransferase (ALT; also called Glutamic Piruvic Transaminase, GPT) is as follows:       The reaction product is piruvate, which proceeds to the Krebs cycle after decarboxylation by piruvate decarboxylase. The reactions catalyzed by transaminases tend to accumulate glutamic acid and to subtract α-ketoglutarate from the Krebs cycle. Recovery of α-ketoglutarate is achieved by oxidative deamination. The reaction, catalyzed by glutamate dehydrogenase, releases free ammonia:       α-aminoacids are thus converted to the corresponding α-ketoacids, and their amino group is incorporated into glutamate. As we shall describe in detail below, in all mammals half the glutamate is processed by glutamate dehydrogenase and its nitrogen released as ammonia; the other half is used as a donor of ammonia to oxalacetate, which is converted to aspartate.       Some animals (notably fishes) eliminate ammonia in the urine: they are defined ammoniotelic (or ammonotelic). Unfortunately, ammonia is basic and at high concentration it is toxic for the renal tubules: thus animals not living in water must convert this compound to something less toxic in order to be able to concentrate it in the urine a to save water. Mammals are defined ureotelic because they use urea as the terminal metabolyte of nitrogen, and their blood and urine contain this compound as the main source of non-protein nitrogen. The transformation of ammonia into urea is carried out by the liver, via a metabolyc pathway called the urea cycle:       The urea cycle occurs partly in the mitochondrion and partly in the cytoplasm. 90% of urea is produced by the liver; the remaining 10% by other organs, notably the kidneys. The first reaction (catalyzed by the ezyme carbamoyl phosphate synthetase, in the mitochondrion) uses bicarbonate, ammonia and 2 molecules of ATP to produce the high energy intermediate carbamoyl phosphate. Carbamoyl phosphate is then combined with a molecule of the non-proteic aminoacid ornithine to produce the non-proteic aminoacid citrulline; the enzyme is called Ornithine transcarbamoylase and the reaction occurs in the mitochondrion. Citrulline is then transferred to the cytoplasm by the citrulline-ornithine antiporter. In the cytoplasm Citrulline is combined with a molecule of aspartic acid by the enzyme Arginino-succnate synthetase; the product is argininosuccinic acid. The enzyme Arginino-succinate lyase breaks down this molecule to yield arginine (a proteic aminoacid) and fumarate (a Krebs cycle metabolyte). Arginase, the last enzyme of the cycle hydrolyzes a C-N bond of arginine to produce urea and ornithine, than can be transported back to the mitochondrion and used in a new cycle. Fumaric acid can be converted to oxalacetic acid in the cytoplasm and then trasferred to the mitochondrion for uage in the Krebs cycle.       The overall balance of the urea cycle (neglecting the consumption of 3 ATP) is as follows:       An interesting observation is that only one of the nitrogens of urea comes from ammonia (via glutamate dehydrogenase); the other derives from one molecule of aspartic acid. Clearly aspartic acid is not enough to sustain the urea cycle: it accounts for only some 7% of the total aminoacids of alimentary proteins. Where does aspartic acid come from? The amino groups of all aminoacids are transferred to α-ketoglutarate by the corresponding aminotransferase, and aspartate is no exception. However the transaminase reactions are all reversible and in the case of Aspartate Aminotransferase (AST; also called Glutamate Oxaloacetate Transaminase, GOT) the reaction flows mainly backwards:       As a consequence, aspartate is produced from glutamate and oxaloacetate (a Krebs cycle metabolic intermediate) and the two nitrogens of the molecule of urea derive from all aminoacids that our organism catabolyzes, via transamination to glutamate and aspartate, as schematically depicted in the figure below that shows the flow of nitrogen from aminoacids to urea (in red the key metabolytes). Audio: Metabolism of ammonia       The α-ketoacids obtained from transamination are further metabolized and are converted to acetyl-CoA or to intermediates of the glycolysis or the Krebs cycle. The relationships between these catabolic pathways is fascinating (but quite intricated):       Biosynthesis of ornithine. As a general rule we obtain from our diet more aminoacids than we need for protein turnover and use part of them catabolically, to fuel the Krebs cycle. This consideration, however, only applies to proteic aminoacid: our diet does not contain any significant amount of non-proteic aminoacids. Thus non-proteic aminoacids, such as ornithine or citrulline must be synthesized by our metabolism. Ornithine is synthesized from glutamic acid, in a pathway: that requires glutamic semialdehyde as an intermediate (produced by glutamate 5-reductase) and its transamination (catalyzed by ornithine transaminase). Alternatively, if escess arginine is available, it can be converted to ornithine by arginase. MEASUREMENT OF BLOOD UREA NITROGEN (BUN) AND RELATED PARAMETERS       Nitrogen is contained in the blood in two major forms: urea and proteins. Less relevant sources are free ammonia, free aminoacids, hormones and creatinine. The normal range for BUN is 6-20 mg/dL. It is important to remark that, given the chemical formula of urea (H4CN2O, MW=60) and its nitrogen content (47% w/w), 6-20 mg/dL of BUN correspond to 13-43 mg/dL urea.       The easiest methods to determine BUN are enzymatic or colorimetric. The classical colorimetric method takes advantage of the reagent diacetyle that selectively reacts with urea forming a yellow diazinic derivative (diacetylurea). Since diacetyle is unstable the reaction starts from its precursor diacetylmonoxime, which in acidic buffers forms diacetyle. The enzymatic method is as follows: (i) serum is obtained from venous puncture; it may be de-proteinized using TCA precipitation followed by neutralization. (ii) The concentration of free ammonia is selectively measured using the appropriate electrode. (iii) The bacterial enzyme urease is added to the sample; it catalyzes the decomposition of urea to carbon dioxide and ammonia: CO(NH2)2 + H2O --> CO2 + 2 NH3. (iv) The concentration of ammonia is again determined with the same electrode; BUN corresponds to the increase of ammonia concentration after addition of urease. Alternatively, ammonia can be measured enzymatically, using α-ketoglutarate, NADPH, and glutamate dehydrogenase; the reaction is the inverse of that catalyzed by the enzyme under physiological conditions, and the signal is provided by the absorbance change odf NADPH. For a description of this and other enzymetic methods see this link.       In alternative several colorimetric methods are available, based on the Berthelot's reaction: urea is degraded to carbon dioxide and ammonia by urease and ammonia is allowed to react with hypochlorite and phenol (in the presence of a catalyst) to yield the blue compound indophenol, whose concentration can be determined by absorbance spectrophotometry.       Increased urea concentration in the blood is usually due to impaired kidney function. The kidney function may be assessed by measuring the Glomerular Filtration Rate (GFR, see the lecture on electrolytes), using creatinine, the second most important low-molecular weight nitrogen containing compound in the blood, as a tracer. In the healthy adult its serum concentration is 0.5-1.2 mg/dL (or 50-110 μMol/L). Reference values for low molecular weigth nitrogen-containing compounds in human plasma urea < 20 mg/dL by nitrogen (< 43 mg/dL for urea molecule; < 7 mMol/L) creatinine < 1.2 mg/dL (< 110 μMol/L) ammonia < 50 μMol/L (in newborns and infants < 150-200 μMol/L) DISTURBANCES OF THE UREA CYCLE       It is perhaps surprising that a metabolism so fundamental as the urea cycle is so prone to severe genetic defects, given that these diseases usually cause early death and are strongly counter selected. However one should consider that (i) insufficiency of dissimilatory pathways (such as the urea cycle) is usually silent in the foetus, as the mother body takes care of the excretion of the accumulated metabolyte; and (ii) these diseases are recessive and in some cases X-linked; thus the affected genes are to some extent protected from severe selection.       As a general rule, ereditary defects of the urea cycle become evident in the newborn, and have a very severe prognosis, survival beyond the infantile age being uncommon. They are inherited as autosomal recessive traits, with the exception of the deficiency of ornithine transcarbamoylase that is recessive and X-linked. The symptoms of these defects are essentially the same: no matter which enzyme is involved, hyperammoniemia is constantly present and is the leading cause of the clinical symptoms: mental retardation, coma, and death. Seizures and vomiting are often observed. The normal value of ammoniemia in the adult's blood is < 50 μMol/L; in the newborn it may be up to 150-200 μMol/L because of the incomplete maturity of the liver. In addition to hyperammoniemia, genetic defects of the urea cycle may cause some specific aminoacid to appear in the blood and urine at abnormally high concentrations (e.g. citrullinemia, argininosuccinic acidemia, argininemia). Diagnosis is suspected on the basis of clinical findings and demonstration of hyperammoniemia, and confirmed by gene sequencing. Defects of the urea cycle Disease name Enzymatic defect Organs affected and symptoms Deficiency of Carbamoyl phosphate synthetase   Hyperammoniemia, vomiting, mental retardation, coma and death Deficiency of N-acetyl glytamate synthase (N-acetyl glutamate is a required allosteric activator of carbamoyl phosphate synthase)   Simlar to the deficiency of Carbamoyl phosphate synthetase Deficiency of Ornithine transcarbamoylase   Hyperammoniemia, vomiting, mental retardation, coma and death (X-linked; lethal in the male) Citrullinemia Deficiency of Argininosuccinate synthetase Hyperammoniemia, vomiting, mental retardation, coma and death Type II citrullinemia (adult onset) Deficiency of the Aspartate/Glutamate carrier 2 (AGC2, citrin), a mitochondrial transporter Similar to, but less severe than, citrullinemia. Patients usually reach adulthood. Crises of hyperammonemia may be precipitated by carbohydrate intake Argininosuccinic acidemia Deficiency of Argininosuccinate lyase Hyperammoniemia, vomiting, mental retardation, coma and death Argininemia Deficiency of Argininase Hyperammoniemia, convulsions, spasticity, mental retardation, coma and death Ornithinemia Homocitrullinuria syndorme Deficiency of ornithine-citrulline antiporter Hyperammoniemia, convulsions, spasticity, mental retardation, coma and death Deficiency of ornithine transaminase   Blindness; possible hyperammoniemia of variable severity, mental defects Audio: Hereditary defects of the urea cycle OTHER METABOLIC PATWAYS THAT UTILIZE AMMONIA; DIFFERENTIAL DIAGNOSIS OF HYPERAMMONEMIAS       The urea cycle uses up to 80 or 90% of the ammonia derived from aminoacid metabolism, either as ammonia or aspartate. The remaining fraction of ammonia is utilized by other metabolic pathways, that produce aminoacids. Examples are the biosynthesis of Glycine by Gly synthase and that of Glutamine by Gln synthase. Because of these additional pathways, genetic defects of the urea cycle are not the only possible cause of hyperammonemia, and milder, but still symptomatic, levels of hyperammonemia may be observed in several genetic defects of aminoacid byosynthesis. Moreover, glutamine, like aspartate, is a common donor of ammonia for the biosynthesis of nucleotides: for example the conversion of UTP to CTP utilized Gln as the donor of amine group. As a consequence, the (rare) genetic defect of Gln synthase may cause the accumulation of nucleotide base precursors whose further conversion is prevented by lack of Gln.       The differential diagnosis of hyperammonemias relies on the identification of other metabolytes that may be present in excess or in defect; these may be intermediates of the urea cycle (e.g. argininosuccinic acid), or intermediates of other pathways. Differential diagnosis of hyperammonemias In the adult In the newborn Acute or chronic liver failure (due to viral hepatitis, cirrhosis, intoxication, etc.) Sepsis, enteritis (NH3 produced by bacteria; inactivation of Gln synthase) Inherited defects of the ammonia cycle Inherited defects of Gln synthase Inherited defects of organic acid metabolism Liver prematurity       Some important associations may be noticed: hyperammonemia may be associated to abnormal levels of nucleotide biosynthesis intermediates (e.g. orotic acid) or intermediates of the aminoacid catabolism. These associations are usually mediated by the leakage to the cytoplasm of carbamoyl phosphate accumulated in the mitochondrion because of the blockade of the urea cycle. Remember that under physiological conditions the carbamoyl phosphate required for pyridine nucleotide biosynthesis is produced by the cytoplasmic synthase, that for the urea cycle by the mitochondrial synthase; only under pathological conditions does mitochondrial carbamoyl phosphate leak to the cytoplasm. When this occurs, the biosynthesis of pyrimidine nucleotides is stimulated, leading to an atypical form of orotic aciduria (to be distinguished from the usual form, due to a genetic defect of orotate PRPP transferase), in which hyperammonemia and excess orotic acid are both present. Defects of the metabolism of aminoacids and other organic acids may cause hyperammonemia by interfering with the mitochondrial transport or by inhibiting enzymes relevant to the urea cycle (e.g. propionyl-CoA inhibits carbamoyl phosphate synthase I). A list of the metabolic defects that may be associated to hyperammonemia includes: propionic acidemia (defect of propionyl-CoA carboxylase) and methylmalonic acidemia (defect of methylmalonyl-CoA mutase); isovaleric acidemia; and glutaric acidemia. In all these cases, a hemogas analysis is indicated because it may reveal the coexistence of hyperammonemia and metabolic acidosis with increased anion gap. The differential diagnosis is important because some of these defects may respond to dietary and vitamin treatment. UREA AND ORGAN PATHOLOGY       Urea is produced by the liver (for over 90%; other organs, notably the kidney produce less than 10%) and excreted in the urine by the kidney.      Advanced states of liver failure may cause reduced production of urea and low BUN, unless reduced kidney function is also present (see the lecture on bilirubin and liver function). This condition is only observed when the liver function is compromised to a great extent, because the ability of the liver to produce urea greatly exceeds the normal body requirements. Thus ther symptoms of liver failure will be present and will preceed the reduced biosynthesis of urea: hyperbilirubinemia with jaundice, reduced production of serum proteins (hypoalbuminemia), etc. Reduced production of urea is accompanied by hyperammoniemia, with the symptoms and laboratory signs described above. The other possible causes of reduced urea production are the inherited enzymatic diseases listed above. These are diagnosed shortly after birth, thus are neonatal diagnoses, not to be considered in adult patients. Hyperammonemia and encefalopathy are invariably present.       Increased BUN usually points to kidney failure, and indicates measurement of renal function. Since urea and creatinine are cleared by the kidney, an increase of the serum concentration of these substances is usually indicative of kideny disfunction. Azotemia is essentially a synonimous of BUN, and hyperazotemia is the clinical condition in which azotemia is increased above normal values.       Creatinine clearance. The kidney's ability to excrete creatinine is easily measured and provides an important estimate of the organ's function. The method takes advantage of the almost constant concentration of creatinine in the serum, due to the constant rates of production and excretion. A sample of urine is collected over a precisely measured time (e.g. one hour), preferably by a catheter. The concentration of creatinine is measured in the serum and in the urine. Given that the volume of urine can be precisely determined, one can calculate the moles or milligrams of creatinine excreted in one minute by the kidneys: moles of creatinine excreted / minute = [urinary creatinine] x volume of urine / time The amount of creatinine thus calculated was contained in the volume of serum filtered by the kidneys in one minute, i.e.: volume of serum filtered / minute = moles of creatinine excreted in one minute / [serum creatinine]       The normal clearance of creatinine is 90-120 mL / minute; since creatinine is neither reabsorbed nor excreted by the renal tubuli, this value equals the volume of serum filtered by the glomeruli in one minute (Glomerular Filtration Rate, GFR; see the lecture on electrolyte balance). The GFR decreases physiologically with age, and in patients above 70 it is not uncommon to find GFR values of 60 mL/min. Renal atrophy, polycystic kidney disease, glomerulonephritis, aterosclerotic kidney disease are common causes of reduced glomerular filtration. It is important to remark that the volume of urine produced in one minute is highly variable and does not provide any information on glomerular filtration: the kidney can reabsorb up to 99% of the filtered water, depending on the amount of water the patient drinks and the osmotic effect of urine solutes. Further readings Savy et al. Acute pediatric hyperammonemia: current diagnosis and management strategies. Hepat Med. 2018; 10: 105–115. This article contains a good flowchart for the differential diagnosis of hyperammonemia in the newborn. J Häberle, A Chakrapani, N Ah Mew, and N Longo Hyperammonaemia in classic organic acidaemias: a review of the literature and two case histories DB Flannery, YE Hsia, B Wolf Current status of hyperammonemic syndromes. Hepatology 1982; 2: 495-506. SC Sreenath Nagamani, A Erez, and B Lee Argininosuccinate Lyase Deficiency. P. Ferenci Hepatic encephalopathy Gastroenterol. Rep. 2017; 5: 138–147. Questions and exercises: 1) Hyperammoniemia suggests: An hereditary defect in aminoacid metabolism An hereditary defect of the urea cycle An hereditary defect of aminoacid transport 2) 50 mg/dL blood urea nitrogen (BUN) suggests: nothing: the value is within normal limits The value is too low and points to a genetic defect of the urea cycle The value is too high and suggests kidney disease and reduced urinary excretion of urea 3) The normal value of glomerular filtration rate (GFR) is 60-90 mL/min 90-120 mL/min 120-150 mL/min 4) All genetic defects of the urea cycle are inherited as autosomal recessive traits, except for the following one, which is sex-linked: deficiency of ornythine transcarbamoylase citrullinemia arginino succinic acidemia your score: 10 Attendance not registered because of insufficient score - Retry! You can type in a comment or question below (max. length=160 chars.); please specifiy that the subject of your comment or question is aminoacid metabolism: All comments posted on the different subjects have been edited and moved to this web page (for optimal reading try to have at least 80 characters per line)! Thank you Professor (lecture on bilirubin and jaundice). The fourth recorded part, the one on hyper and hypoglycemias is not working. Bellelli: I checked and in my computer it seems to work. Can you better specify the problem you observe? This Presentation (electrolytes and blood pH) feels longer than previous lectures Bellelli: it is indeed. Some subjects require more information than others. I was thinking of splitting it in two nest year. Bellelli in response to a question raised by email: when we compare the blood pH with the standard pH we do not mean to compare the "normal" blood pH (7.4) with the standard pH. Rather we compare the actual blood pH of the patient, with the pH of the same blood sample equilibrated under standard conditions. Thus, if we say that standard pH is lower than pH we mean that equilibriation with 40 mmHg CO2 has caused absorption of CO2 and has lowered the pH with respect to its value before equilibration. (Lipoproteins) Is the production of leptin an indirect cause of type 2 diabetes since it works as a stimulus to have more adipose tissue that produces hormones? Bellelli: in a sense yes, sustained increase of leptin causes the hypothalamus to adapt and to stop responding. Obesity ensues and this in turn may cause an increase in the production of resistin and other insulin-suppressing protein hormones produced by the adipose tissue. However, this is quite an indirect link, and most probably other factors contribute as well. (Urea cycle) what is the meaning of "dissimilatory pathway"? Bellelli: a dissimilatory pathway is a catabolic pathway whose function is not to produce energy, but to produce some terminal metabolyte that must be excreted. Dissimilatory pathways are necessary for those metabolytes that cannot be excreted as such by the kidney or the liver because they are toxic or poorly soluble. Examples of metabolytes that require transformation before being eliminated are heme-bilirubin, ammonia, sulfur and nitrogen oxides, etc. Talking about IDDM linked neuropathy can be the C peptide absence considered a cause of it?? Bellelli: The C peptide released during the maturation of insulin, besides being an indicator of the severity of diabetes, plays some incompletely understood physiological roles. For example it has been hypothesized that it may play a role in the reparation of the atherosclerotic damage of the small arteries. Thus said, I am not aware that it plays a direct role in preventing diabetic polyneuropathy. Diabetic neuropathy has at least two causes: the microvascular damage of the arteries of the nerve (the vasa nervorum), and a direct effect of hyperglycemia and decreased and irregular insulin supply on the nerve metabolism. Diabetic neuropathy is observed in both IDDM and NIDDM, and requires several years to develop. Since the levels of the C peptide differ in IDDM and NIDDM, this would suggest that the role of the C peptide in diabetic neuropathy is not a major one. If you do have better information please share it on this site! In acute intermitted porphyria and congenital erythropoietic porphyria why do the end product of the affected enzymes accumulate instead of their substrate?? Bellelli: First of all, congratulations! This is an excellent question. Remember that a condition is which the heme is not produced is lethal in the foetus; thus the affected enzyme(s) must maintain some functionality for the patient to be born and to come to medical attention. All known genetic defects of heme biosynthesis derange but do not block this metabolic pathway. Congenital Erythropoietc Porphyria (CEP) is a genetic defect of uroporphyrinogen III cosynthase. This protein associates to uroporphyrinogen synthase (which is present and functional in CEP) and guarantees that the appropriate uroporphyrinogen isomer is produced (i.e. uroporphyrinogen III). In the absence of a functional uroporphyrinogen III cosynthase other possible isomers of uroporphyrinogen are produced together with uroporpyrinogen III, mostly uroporphyrinogen I. The isomers of uroporphyrinogen that are produced differ because of the positions of propionate and acetate side chains, and this in turn is due to the pseudo symmetric structure of porphobilinogen. Only isomer III can be further used to produce protoporphyrin IX. Thus in the case of CEP we observe accumulation of abnormal uroporphyrinogen derivatives, which, as you correctly observed are the products of the enzymatic synthesis operated by uroporphyrinogen synthase. The case of Acute Intermittent Porphyria (AIP) is similar, although there may be variants of this disease. What happens is that either the affected enzyme is a variant that does not properly associate with uroporphyrinogen III cosynthase or presents active site mutations that impair the proper alignement of the phoprphobilinogen substrates. In either case abnormal isomers of uroporphyrinogen are produced, as in CEP. Also remark that in both AIP and CEP we observe accumulation of the porphobilinogen precursor: this is because the overall efficiency of the biosynthesis of uroporphyrinogens is reduced. Thus: (i) less uroporphyrinogen is produced, and (ii) only a fraction of the uroporphyrinogen that is produced is the correct isomer (uroporphyrinogen III). is it possible to take gulonolactone oxidase to synthesize vitamin C instead of vitamin C supplement? Bellelli: no, this approach does not work. The main reason is that the biosynthesis of vitamin C, as almost all other metabolic processes, occurs intracellularly. If you administer the enzyme it will at most reach the extracellular fluid but will not be transported inside the cells to any significant extent. Besides, there are other problems in this type of therapy (e.g. the enzyme if administered orally, may be degraded by digestive proteases; if administered parenterally, may cause the immune system to react against a non-self protein). In theory one could think of a genetic modification of the inactive human gene of gulonolactone oxidase, but the risk and cost of this intervention would not be justified. In addition to these considerations, except for cases of shipwreckage or other catastrophes, a proper diet or administration of tablets of vitamin C is effective, risk-free and unexpensive, thus no alternative therapy is reasonable. However, I express my congratulations for your search on the biosynthesis pathway of ascorbic acid. Resorption and not reabsorption would lead to hypercalcemia ie bone matrix being broken down. Bellelli: I am not sure to interpret your question correctly. Resorption indicates destruction of the bone matrix and release of calcium and phosphate in the blood, thus it causes an increase of calcemia. Reabsorption usually means active transport of calcium from the renal tubuli to the blood, thus it prevents calcium loss. It prevents hypocalcemia, and thus complement bone resorption. To avoid confusion it is better use the terms "bone resorption" and " renal reabsorption of calcium". If you have a defect in renal reabsorption, parthyroid hormone will be released to maintain a normal calcium level by means of bone resorption; the drawback is osteoporosis. In Reed and Frost model: I haven't understood what is the relationship between K and R reproductive index. Thank you Professor! Bellelli: in the Reed and Frost model K is the theoretical upper limit of R0. R the reproductive index is the ratio (new cases)/(old cases) measured after one serial generation time. R0 is the value of R one measures at the beginning of the epidemics, when in principle all the population is susceptible. What is the link between nucleotide metabolism and immunodeficiencies and mental retardation? Bellelli: the links may be quite complex, but the principal ones are as follows: 1) the immune response requires a replication burst of granulocytes and lymphocytes, which in turn requires a sudden increase of nucleotide production, necessary for DNA replication. Defects of nucleotide metabolism impair this phase of the immune defense. Notice that the mechanism is similar to the one responsible of anemia which requires a sustained biosynthesis of nucleotides at a constant rate, rather than in a burst. 2) Mental retardation is mainly due to the accumulation of nulceotide precursors in the brain of the newborn, due to the incompletely competent blood-brain barrier. How can ornithine transaminase defects cause hyperammonemia? Is it due to the accumulation of ornithine that blocks the urea cycle or for other reasons? Bellelli: ornithine transaminase is required for the reversible interconversion of ornithine and proline, and thus participates to both the biosynthesis and degradation of ornithine. The enzyme is synthesized in the cytoplasm and imported in the mitochondrion. Depending on the metabolic conditions the deficiency of this enzyme may cause both excess (when degradation would be necessary) or defect (when biosynthesis would be necessary) of ornithine; in the latter case, the urea cycle slows down. Thus there is the paradoxical condition in which alternation may occur between episodes of hyperammonemia and of hyperornithinemia. When we use the Berthelot's reaction to measure BUN do we also have to measure the concentration of free ammonia before adding urease? Bellelli: yes, in principle you should. Berthelot's reaction detects ammonia, thus one should take two identical volumes of serum, use one to measure free ammonia, the other to add urease and measure free ammonia plus ammonia released by urea. BUN is obtained by difference. However, free ammonia in our blood is so much lower than urea that you may omit the first sample, if you only want to measure BUN. Why do we have abnormal electrolytes in hematological neoplasia e.g. leukemia? Bellelli: I do not have a good explanation for this effect, which may have multiple causes. However, you should consider two factors: (i) acute leukemias cause a massive proliferation of leukocytes (or lymphocytes depending on the cell type affected) with a very shortened lifetime; thus you observe an excess death rate of the neoplastic cells. The dying cells release in the bloodstream their content, which has an electrolyte composition different from that of plasma: the cell cytoplasm is rich in K and poor in Na, thus causing hyperkalemia. (ii) the kidney may be affected by the accumulation of neoplastic white cells or their lytic products. Gaussian curve: If it is bimodal is it more likely to be a "certain diagnosis" than if it is unimodal or does it only show the distinguishment from health? Bellelli an obviously bimodal Gaussian curve indicates that the disease is clearly separated from health: usually it is a matter of how precise and clear-cut is the definition of the disease. For example tuberculosis is the disease caused by M. tuberculosis, thus if the culture of the sputum is positive for this bacterium you have a "certain" diagnosis (caution: the patient may suffer of two diseases, e.g. tuberculosis and COPD diagnosis of the first does not exclude the second). However, in order to have a "certain" diagnosis it is not enough that distribution of the parameter is bimodal, it is also required that the patient's parameter is out of the range of the healthy condition: this is because a distribution can be bimodal even though it is composed by two Gaussians that present a large overlap, and the patient's parameter may fall in the overlapping region. Thus, in order to obtain a "certain" diagnosis you need to consider not only the distribution of the parameter(s) but also the patient's values and the extent of the overlapping region. Prof can you please elaborate a bit more on the interhuman variability and its difference with the interpopulation variability please? Bellelli: every individual is a unique combination of different alleles of the same genes; this is the source of interindividual variability. Every population is a group of individuals who intermarry and share the same gene pool (better: allele pool). Every allele in a population has its own frequency. Two population may differ because of the diffferent frequencies of the same alleles; in some cases one population may completely lack some alleles. The number and frequencies of alleles of each gene determine the variance. If you take two populations and calculate the cumulative interindividual variance of the population the number you obtain is the sum of two contributions: the interindividual variance within each population, plus the interpopulation variance between the means of the allele frequencies. For example, there are human population in which the frequency of blood group B is close to 0% and other populati ons in which it is 30% or more. Prof can you please explain again the graph you have showed us in class about thromboplastin? (Y axis=abs X axis= time) Bellelli: the graph that I crudely sketched in class represented the signal of the instrument (an absorbance spectrophotometer) used to record the turbidity of the sample (turbidimetry). The plasma is more or less transparent, before coagulation starts. When calcium and the tissue factor (or collagen) are added. thrombin is activated and begins digesting fibrinogen to fibrin; then fibrin aggregates. The macroscopic fibrin aggregates cause the sample to become turbid, which means it scatters the incident light. The instrument reads this as a decrease of transmitted light (i.re an increase of the apparent absorbance) and the time profile of the signal presents an initial lag phase, which is called the protrombin or thromboplastin time depending on the component which was added to start coagulation (tissue factor or collagen). Prof can you please explain the concept you have described in class about the simultaneous hypercoagulation and hemorrhagic syndrome? How can this occur? Bellelli: The condition you describe is observed only in the Disseminated Intravascular Coagulation syndrome. Suppose that the patient experiences an episode of acute pancreatitis: tripsin and chymotripsin are reabsorbed in the blood and proteolytically activate coagulation causing an extensive consumption of fibrinogen and other coagulation factors. Tripsin and chymotripsin also damage the vessel walls and may cause internal hemorrages, but at that point the consumption of fibrinogen may have been so massive that not enough is left to form the clot where the vessel has been damaged, causing an internal hemorrage. Pancreatitis is a very severe, potentially lethal condition, and DIC is only one of the reasons of its severity. You said that certain drugs (ethanol, cocaine, cannabis, opiates...) cause a necessity of higher and higher dosage, for two reasons: the enzyme in the liver is inducible and the receptors in the brain are expressed less and less. So, first, I am not sure I got it right, and second I did not understand how expressing less receptors leads to a necessity of higher dosage. Bellelli: You got it correctly, but the detailed mechanism of resistance may vary among different substances, and not all drugs cause adaptation. The reason why reducing the number of receptors may require an increased dosage of the drug is as follows: suppose that a certain cell has 10,000 receptors for a drug. When bound to its agonist/effector, each receptor produces an intracellular second messenger. Suppose that in order for the cell to respond 1,000 receptors must be activated. The concentration of the effector required is thus the concentration that produces 10% saturation. You can easily calculate that this concentration is approximately 1/10 of the equilibrium dissociation constant of the receptor-effector complex (its Kd), the law being Fraction bound = [X] / ([X]+Kd) where [X] is the concentration of the free drug. After repeated administration, the subject becomes adapted to the drug, and his/her cells express less receptors, say 5,000. The cell response will in any case require that 1,000 receptors are bound to the effector and activated, but this now represents 20% of the total receptors, instead of 10%. The drug concentration required is now 1/4 of the Kd. Continuing administration of the drug further reduces the cell receptors, but the absolute number of activated receptors required to start the response is constant; thus the fewer receptors on the cell membrane, the higher the fraction of activated receptors required. Why does hyperosmolarity happen in type 2 diabetes and not in type 1? Bellelli: Hyperosmolarity can occur also in type 1 diabetes, albeit infrequently. The approximate formula for plasma osmolarity is reported in the lecture on electrolytes: osmolarity = 2 x (Na+ + K+) + BUN/2.8 + glucose/18 this is expressed in the usual clinical laboratory units (mEq/L for electrolytes, g/dL for non- electrolytes). The normal values are: osmolarity = 2 x (135 + 5) + 15/2.8 + 100/18 = 280 + 5.4 + 5.6 = 291 mOsmol/L Let's imagine a diabetic patient having normal values for electrolytes and BUN, and glycemia=400 mg/dL: osmolarity = 280 + 5.4 + 22.4 = 307.8 mOsmol/L The hyperosmolarity in diabetes is mainly due to hyperglycemia, even though other factors may contribute (e.g. diabetic nefropathy); however the contribution of glucose to osmolarity is relatively small. As a consequence in order to observe hyperosmolarity the hyperglycemia should be extremely high; this is more often observed in type 2 than in type 1 diabetes, for several reasons, the most relevant of which is that in type 1 diabetes all cells are starved of glucose, and the global reserve of glycogen in the body is impoverished: there is too much glucose in the blood and too few everywhere else, thus reducing, but not abolishing, the risk of extreme hyperglycemia. Usually in type 2 diabetes the glycogen reserve in the organism is not impoverished, thus the risk of extreme hyperglycemia is higher. Hemostasis and Thrombosis lecture: I don't understand why is sodium citrate added to the serum solution to measure the prothrombin time. Bellelli: in order to measure PT or PTT you want to be able to start the coagulation process at an arbitrary time zero, and measure the increase in turbidity of the serum sample. To do so you need (i) to prevent spontaneous coagulation with an anticoagulant; and (ii) to be able to overcome the anticoagulant at your will. Citrate (or oxaloacetate; or EDTA) has the required characteristics: it chelates calcium, and in this way it prevents coagulation; but you can revert its effect at your will by adding CaCl2 in excess to the amount of citrate. You cannot obtain the same effect with other anticoagulants (e.g. heparin) whose action cannot be easily overcome. Dear professor I cannot do the self evaluation test because it says the the time has expired It is not possible because I havent even started them Bellelli: this is due to the fact that the program registers your name and matricola number from previous attempts. I shall fix this bug. Meanwhile try to use a fake matricola number. How is nephrotic syndrome associated hypoalbuminemia as you described in methods of analysis of protein because seems counterintuitive Bellelli: nephrotic syndrome is an autoimmune disease in which the glomerulus is damaged and the filtration barrier is disrupted; diuresis is normal but there is loss of proteins (mostly albumin) in the urine. I m sorry i confused polyurea with hypoalbuminemia but my question still stands during glomerulonephritis you mentioned something of polyurea as compensation i could not follow how this compensation mechanism works and collapse after some time in glomerulonephritis Bellelli: the condition you describe is NOT characteristic of acute glomerulonephritis. In glomerulonephritis there is damage of the glomerulus and severely impaired GFR. Thus the diuresis is severely reduced, and due to impaired filtration proteins appear in the urine. The condition you describe corresponds to the initial stage of chronic kidney failure, usually due to atherosclerosis, diabetes, hypertension or other type of damage of the kidney tissue. In this case GFR is impaired, albeit to a lesser extent than in glomerulonephritis, and the excretion of urea is reduced. This leads to increased BUN. However the increased concentration of urea reduces the ability of the tubuli to reabsorb water, because of osmotic reasons, yielding compensatory polyuria. The patient has reduced GFR but normal or increased diuresis (urine volume in 24 hours). To some extent this effect is beneficial, as it favors the elimination of urea; however it cannot completely solve the problem and in any case the progression of the disease leads to kidney insufficiency. In its essence the point is that a moderately reduced GFR can be partially compensated by reduced tubular reabsorption; a severely reduced GFR cannot. Lecture on Hemogas analysis interpretation of complex cases standard pH Why if PCO2 is less than 40 mmHg it is absorbed during equilibration? Thank you in advance Bellelli: if PCO2 of the patient's blood sample is less than 40 mmHg, when the machine equilibrates with 40 mmHg CO2 the gas is absorbed: i.e. the new PCO2 becomes 40 mmHg and the total CO2 of the sample increases; as CO2 is the acid of the buffer, the standard pH (in this case) decreases, whereas standard bicarbonate will slightly increase. Professor I don't understand how we arrive to this formula: Accuracy = sensitivity x prevalence specificity x (1-prevalence) Bellelli: ok, this relationship is poorly explained in your text, I shall improve its explanation. We use the following definitions: prevalence = sick individuals / total population; accuracy = (true+ + true-) / total population; sensitivity = true+ / sick individuals = true+ / total population x prevalence; specificity = true- / healthy individuals = true- / total population x (1-prevalence); thus we can rewrite: sensitivity x prevalence = true+ / total population; specificity x (1-prevalence) = true- / total population; accuracy = sensitivity x prevalence + specificity x (1-prevalence) Why do we use RNA primer in PCR and not DNA primers? I thought the beginning of the sequence of the gene segment that is going to be formed is made of DNA Bellelli: DNA polimerases require the RNA primers that are synthesized by the enzyme primase. DNA primers do not exist in vivo and would not be recognized by DNA polimerases.       Home of this course Slides of this lecture