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'''''[[Clostridium difficile]]''''' is a spore-forming, anaerobic, toxin-producing bacterium that is a "common inhabitant of the colon flora in human infants and sometimes in adults. It produces a toxin that causes pseudomembranous enterocolitis in patients receiving antibiotic therapy." ''C. difficile'' superinfection after oral antibiotic therapy, leading to potentially fatal pseudomembranous enterocolitis, has been an increasingly severe public health problem. Indeed, many primary physicians now consider it wise to warn outpatients on antibiotics to seek immediate consultation if they develop severe diarrhea.
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C. difficile is present at low levels in the gut flora of about 3% of adults. These people however show no symptoms and do not need to be treated. The infection occurs when a person is treated with antibiotics targeted against other bacteria. The disease is for the most part nosocomial. Patients who are hospitalized come in contact and are often inoculated with the bacteria. When the patient is treated with antibiotics, especially those with a broad range of activity, the normal gut flora is disrupted, and C. difficile, with its multi-drug resistance, experiences overgrowth. The bacteria releases large quantities of enterotoxins (toxin A) and cytotoxins (toxin B), causing pseudomembranous enterocolitis.
==Footnotes==
 
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[[Image:img2.gif|thumb|left|250px|scanning electron micrograph of C. difficile]]
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====History====
In 1935, Hall and O’Toole first isolated the bacteria from the stools of newborns and described it. They named it ''Bacillus difficilis'' because it was hard to isolate and grew very slowly in culture.
 
C. difficile is an important pathogen that is currently increasing in its prevalence world-wide. A complete genome sequence would enable geneticists to come up with a more direct and efficient treatment against the pathogen. The genetic material encodes for antimicrobial resistance, production of toxins (virulence), host interaction (adaptations for survival and growth within the gut environment), and the production of surface structures. The understanding of how these genes interact with their environment will be useful in developing therapies against C. difficile associated diseases.
 
====Genome Structure====
Sebaihia et al (2006) determined the complete genomic sequence of ''C. difficile'' strain 630, a highly virulent and multidrug-resistant strain. It was found that the genome consists of a circular chromosome of 4,290,252 bp and a plasmid, pCD630, of 7,881 bp. The chromosome encodes 3,776 predicted coding sequences (CDSs), with resistance, virulence, and host interaction genes, while the plasmid carries only 11 CDSs, none of which has any obvious function. ''C. difficile'' has a highly mobile genome, with 11% of the genome consisting of mobile genetic elements, mostly in the form of conjugative transposons. Conjugative transposons are mobile genetic elements that are capable of integrating into and excising from the host genome and transferring themselves, and are responsible for the evolutionary acquisition by C. difficile of genes involved in resistance, virulence, and host interactions. Some of the mobile elements are prophage sequences. Host interaction genes involve genes that code for metabolic capability adaptations for survival and growth within the gut environment.
 
''[[Clostridium difficile|.... (read more)]]''

Latest revision as of 10:19, 11 September 2020

In computational molecular physics and solid state physics, the Born-Oppenheimer approximation is used to separate the quantum mechanical motion of the electrons from the motion of the nuclei. The method relies on the large mass ratio of electrons and nuclei. For instance the lightest nucleus, the hydrogen nucleus, is already 1836 times heavier than an electron. The method is named after Max Born and Robert Oppenheimer[1], who proposed it in 1927.

Rationale

The computation of the energy and wave function of an average-size molecule is a formidable task that is alleviated by the Born-Oppenheimer (BO) approximation.The BO approximation makes it possible to compute the wave function in two less formidable, consecutive, steps. This approximation was proposed in the early days of quantum mechanics by Born and Oppenheimer (1927) and is indispensable in quantum chemistry and ubiquitous in large parts of computational physics.

In the first step of the BO approximation the electronic Schrödinger equation is solved, yielding a wave function depending on electrons only. For benzene this wave function depends on 126 electronic coordinates. During this solution the nuclei are fixed in a certain configuration, very often the equilibrium configuration. If the effects of the quantum mechanical nuclear motion are to be studied, for instance because a vibrational spectrum is required, this electronic computation must be repeated for many different nuclear configurations. The set of electronic energies thus computed becomes a function of the nuclear coordinates. In the second step of the BO approximation this function serves as a potential in a Schrödinger equation containing only the nuclei—for benzene an equation in 36 variables.

The success of the BO approximation is due to the high ratio between nuclear and electronic masses. The approximation is an important tool of quantum chemistry, without it only the lightest molecule, H2, could be handled; all computations of molecular wave functions for larger molecules make use of it. Even in the cases where the BO approximation breaks down, it is used as a point of departure for the computations.

Historical note

The Born-Oppenheimer approximation is named after M. Born and R. Oppenheimer who wrote a paper [Annalen der Physik, vol. 84, pp. 457-484 (1927)] entitled: Zur Quantentheorie der Molekeln (On the Quantum Theory of Molecules). This paper describes the separation of electronic motion, nuclear vibrations, and molecular rotation. A reader of this paper who expects to find clearly delineated the BO approximation—as it is explained above and in most modern textbooks—will be disappointed. The presentation of the BO approximation is well hidden in Taylor expansions (in terms of internal and external nuclear coordinates) of (i) electronic wave functions, (ii) potential energy surfaces and (iii) nuclear kinetic energy terms. Internal coordinates are the relative positions of the nuclei in the molecular equilibrium and their displacements (vibrations) from equilibrium. External coordinates are the position of the center of mass and the orientation of the molecule. The Taylor expansions complicate the theory tremendously and make the derivations very hard to follow. Moreover, knowing that the proper separation of vibrations and rotations was not achieved in this work, but only eight years later [by C. Eckart, Physical Review, vol. 46, pp. 383-387 (1935)] (see Eckart conditions), chemists and molecular physicists are not very much motivated to invest much effort into understanding the work by Born and Oppenheimer, however famous it may be. Although the article still collects many citations each year, it is safe to say that it is not read anymore, except maybe by historians of science.

Footnotes

  1. Wikipedia has an article about Robert Oppenheimer.