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Find video protocols related to scientific articles indexed in Pubmed.
Biochemistry and evolutionary biology: two disciplines that need each other?
J. Biosci.
PUBLISHED: 02-07-2014
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Biochemical information has been crucial for the development of evolutionary biology. On the one hand, the sequence information now appearing is producing a huge increase in the amount of data available for phylogenetic analysis; on the other hand, and perhaps more fundamentally, it allows understanding of the mechanisms that make evolution possible. Less well recognized, but just as important, understanding evolutionary biology is essential for understanding many details of biochemistry that would otherwise be mysterious, such as why the structures of NAD and other coenzymes are far more complicated than their functions would seem to require. Courses of biochemistry should thus pay attention to the essential role of evolution in selecting the molecules of life.
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Michaelis and Menten and the long road to the discovery of cooperativity.
FEBS Lett.
PUBLISHED: 06-16-2013
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This article sketches the road from the establishment of the principles of enzyme kinetics, at the beginning of the 20th century, to the discovery of regulatory mechanisms and the models to explain them, from the middle of the century onwards. A long gap in time separates the two periods, in which technological advances were made that allowed the discovery of feedback inhibition and cooperativity. In particular, these discoveries and the theory needed to explain them could not have been made without knowledge of the major metabolic pathways and the enzymes and metabolites involved in them.
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From LHomme Machine to metabolic closure: steps towards understanding life.
J. Theor. Biol.
PUBLISHED: 02-27-2011
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The nature of life has been a topic of interest from the earliest of times, and efforts to explain it in mechanistic terms date at least from the 18th century. However, the impressive development of molecular biology since the 1950s has tended to have the question put on one side while biologists explore mechanisms in greater and greater detail, with the result that studies of life as such have been confined to a rather small group of researchers who have ignored one anothers work almost completely, often using quite different terminology to present very similar ideas. Central among these ideas is that of closure, which implies that all of the catalysts needed for an organism to stay alive must be produced by the organism itself, relying on nothing apart from food (and hence chemical energy) from outside. The theories that embody this idea to a greater or less degree are known by a variety of names, including (M,R) systems, autopoiesis, the chemoton, the hypercycle, symbiosis, autocatalytic sets, sysers and RAF sets. These are not all the same, but they are not completely different either, and in this review we examine their similarities and differences, with the aim of working towards the formulation of a unified theory of life.
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Specificity of non-Michaelis-Menten enzymes: necessary information for analyzing metabolic pathways.
J Phys Chem B
PUBLISHED: 10-28-2010
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The specificity of an enzyme obeying the Michaelis?Menten equation is normally measured by comparing the kcat/Km for different substrates, but this is inappropriate for enzymes with a Hill coefficient h different from 1. The obvious alternative of generalizing Km in the expression as K0.5, the substrate concentration for half-saturation, is better, but it is not entirely satisfactory either, and here we show that kcat/K0.5(h) gives satisfactory results for analyzing the kinetic behavior of metabolic pathways. The importance of using kcat/K0.5(h) increases with the value of h, but even when h is small, it makes an appreciable difference, as illustrated for the mammalian hexokinases. Reinterpretation of data for the specificity of these enzymes in terms of the proposed definition indicates that hexokinase D, often believed highly specific for glucose, and accordingly called “glucokinase”, actually has the lowest preference for glucose over fructose of the four isoenzymes found in mammals.
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A simple self-maintaining metabolic system: robustness, autocatalysis, bistability.
PLoS Comput. Biol.
PUBLISHED: 02-26-2010
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A living organism must not only organize itself from within; it must also maintain its organization in the face of changes in its environment and degradation of its components. We show here that a simple (M,R)-system consisting of three interlocking catalytic cycles, with every catalyst produced by the system itself, can both establish a non-trivial steady state and maintain this despite continuous loss of the catalysts by irreversible degradation. As long as at least one catalyst is present at a sufficient concentration in the initial state, the others can be produced and maintained. The system shows bistability, because if the amount of catalyst in the initial state is insufficient to reach the non-trivial steady state the system collapses to a trivial steady state in which all fluxes are zero. It is also robust, because if one catalyst is catastrophically lost when the system is in steady state it can recreate the same state. There are three elementary flux modes, but none of them is an enzyme-maintaining mode, the entire network being necessary to maintain the two catalysts.
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A weak link in metabolism: the metabolic capacity for glycine biosynthesis does not satisfy the need for collagen synthesis.
J. Biosci.
PUBLISHED: 11-13-2009
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In a previous paper, we pointed out that the capability to synthesize glycine from serine is constrained by the stoichiometry of the glycine hydroxymethyltransferase reaction, which limits the amount of glycine produced to be no more than equimolar with the amount of C 1 units produced. This constraint predicts a shortage of available glycine if there are no adequate compensating processes. Here, we test this prediction by comparing all reported fl uxes for the production and consumption of glycine in a human adult. Detailed assessment of all possible sources of glycine shows that synthesis from serine accounts for more than 85% of the total, and that the amount of glycine available from synthesis, about 3 g/day, together with that available from the diet, in the range 1.5-3.0 g/day, may fall significantly short of the amount needed for all metabolic uses, including collagen synthesis by about 10 g per day for a 70 kg human. This result supports earlier suggestions in the literature that glycine is a semi-essential amino acid and that it should be taken as a nutritional supplement to guarantee a healthy metabolism.
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Closure to efficient causation, computability and artificial life.
J. Theor. Biol.
PUBLISHED: 05-19-2009
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The major insight in Robert Rosens view of a living organism as an (M,R)-system was the realization that an organism must be "closed to efficient causation", which means that the catalysts needed for its operation must be generated internally. This aspect is not controversial, but there has been confusion and misunderstanding about the logic Rosen used to achieve this closure. In addition, his corollary that an organism is not a mechanism and cannot have simulable models has led to much argument, most of it mathematical in nature and difficult to appreciate. Here we examine some of the mathematical arguments and clarify the conditions for closure.
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Understanding the regulation of aspartate metabolism using a model based on measured kinetic parameters.
Mol. Syst. Biol.
PUBLISHED: 04-16-2009
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The aspartate-derived amino-acid pathway from plants is well suited for analysing the function of the allosteric network of interactions in branched pathways. For this purpose, a detailed kinetic model of the system in the plant model Arabidopsis was constructed on the basis of in vitro kinetic measurements. The data, assembled into a mathematical model, reproduce in vivo measurements and also provide non-intuitive predictions. A crucial result is the identification of allosteric interactions whose function is not to couple demand and supply but to maintain a high independence between fluxes in competing pathways. In addition, the model shows that enzyme isoforms are not functionally redundant, because they contribute unequally to the flux and its regulation. Another result is the identification of the threonine concentration as the most sensitive variable in the system, suggesting a regulatory role for threonine at a higher level of integration.
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Regulation of intestinal morphology and GALT by pituitary hormones in the rat.
Ann. N. Y. Acad. Sci.
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Here, the effects of neurointermediate (NIL), anterior (AL), and total hypophysectomy (HYPOX) on ileal mucosa cells and gut-associated lymphoid tissue (GALT) are reported. Compared with the sham-operated (SHAM) rats, the villi height and goblet cells numbers were significantly decreased in all groups. Lamina propria area decreased in AL and HYPOX, but not in NIL animals. CD8(+) but not CD4(+) lymphocytes decreased in the HYPOX and NIL groups. Paneth cells did not change, while IgA cells, IgM cells, and secretory IgA were significantly decreased in all groups. NIL but not AL animals lost significant numbers of IgA cells and secretory IgA. In summary, pituitary hormones exert lobe-specific regulatory effects on the gut and on GALT.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.