Molecular method

Freeman, A. J., J. Chem. Phys. 28, 230, "Configuration interaction study of the electronic structure of the OH radical by the atomic and molecular methods."... 

In the following examples we will focus on isolated molecules. In these cases, the LDF equations are solved by the molecular method described above using the DMOL/86 program (17). 

Before studying the reactivity of the nanoparticles, it is necessary to evaluate whether the synthetic method employed would lead to particles of clean unoxidized surface, able to react with incoming molecules. For this purpose we used, besides physical techniques (which are sometimes difficult to handle due to the high oxidability of particles prepared in this way), molecular methods, namely IR and NMR spectroscopy, as well as magnetic measurements which can give a precise description of the surface properties of the particles. 

In recent years molecular taxonomic tests have been introduced. There are a number of molecular methods available. However, due to the volume and variety of organisms it is important that any molecular method meet the following criteria ... 

The goal is to achieve a polyphasic taxonomic approach for authentication and quality control of microbial strains. Each morphological, physiological, cytochemical, and molecular method has hmitations. Combining and comparing the results enable us to obtain a more accurate and complete picture of the microorganism s identity. 

Molecular methods used to uncover mutations are subject to several variables. The anticoagulants used for blood collection can affect digestion with restriction enzymes and amplification reactions. The type of detergent used in cell lysis can affect amplification of DNA by inhibiting the DNA-amplifying enzyme such as the taq polymerase used in the polymerase chain reaction (116). The control of contamination is crucial in ensuring the quality of results obtained by molecular analysis (117). 

The practicing clinician has a number of different tests available to aid in the evaluation of patients with suspected hepatitis C. These include measurement of alanine aminotransferase (ALT) levels, liver biopsy, serological tests (ELISA and recombinant immunoblot assay), and molecular methods for detection and quantitation of HCV RNA. 

Wilber, J. C., and Urdea, M. S. (1995). Chapter 6. In Molecular methods for virus detection. Quantification of viral nucleic acids using branched DNA signal amplification. (San Diego Academic Press). 

Baker, C.J.O., Fulthorpe, R.R., and Gilbride, K.A., An assessment of variability of pulp mill wastewater treatment system bacterial communities using molecular methods, Wat. Qual. Res. J. (Canadian), 38, 227-242, 2003. 

Section 2 mainly focuses on the current efforts to improve the accuracy of quantum calculations using simplified empirical model forms. McNamara and Hillier, in Chapter 5, summary their work on improving the description of the interactions in biological systems via their optimized semiempirical molecular models. Piquemal and co-workers present recent advances in the classical molecular methods, aiming at better reproduction of high-level quantum descriptions of the electtostatic interactions in Chapter 6. In Chatper 7, Cui and Elstner describe a different semiempir-... 

Bacterial plant pathogens are usually identified by microscopic observation and comparison of the symptoms on the plant with published descriptions and photographs, but various rapid serological and molecular methods are now being developed for plant disease diagnosis.16,17... 

To ensure the safety of food products, representative samples must be inspected so that foodborne bacteria can be identified.15,18,19 Bacteria producing heat-stable enterotoxins, such as Staphylococcus aureus, may be identified by biochemical and serological techniques.20,21 Molecular methods are now widely used for the identification of many pathogenic foodborne bacteria,15,22,23 In addition bacteria used as starter cultures for cheese, yogurt, other fermented foods and beverages, and probiotic dietary supplements may be identified for quality assurance.22,24,25... 

In a sense, therefore, there have been two conflicting views with respect to the suitability of formalin as a fixative, in the face of demands that biopsy tissues may be examined not only by traditional morphologic methods, but also by IHC, in situ hybridization (ISFI) and, following extraction procedures, by other molecular methods. Both views recognize that these newer methods do not perform well, or at all, on routinely processed FFPE tissues. One view advocates the development of new fixatives that are molecular friendly, the other view holds that AR-based methods may be employed to achieve accurate valid results of IHC, ISH, and other molecular methods using FFPE tissues. 

L. Laiz, G. Pinar, W. Lubitz, C. Saiz Jimenez, Monitoring the colonization of monuments by bacteria cultivation versus molecular methods, Environ. Microbiol., 5, 72 74 (2003). 

Based on the previous publications, azo dye can be reduced by azoreductase-catalyzed reduction under anaerobic conditions. But still there is a speculation whether bacterial flavin reductases are responsible for the azo reductase activity observed with bacterial cell extracts. In a published report, it is reported that flavin reductases are indeed able to act as azo reductases [24]. Bacteria produce extracellular oxidative enzymes, which are relatively nonspecific enzymes catalyzing the oxidation of a variety of dyes. It was reported that so many diverse groups of bacteria play a role in decolorization. It has been also reported that mixed microbial community could reduce various azo dyes, and members of the y-proteabacteria and sulfate reducing bacteria (SRB) were found to be prominent members of mixed bacterial population by using molecular methods to determine the microbial population dynamics [1],... 

Corporeau, C. and Auffret, M., In situ hybridisation for flow cytometry a molecular method for monitoring stress-gene expression in hemolymph cells of oysters, Aquatic Toxicol., 64, 427, 2003. 

ENZ enzyme assays, SC structural composition, MM molecular methods, IL isotopic labeling, IF isotopic fractionation, INH inhibition studies, UNK unknown, LOX lipoxogenase, EPSP synthase 5-enolpyruvylshikimate-3-phosphate, SDH shikimate dehydrogenase, PAL phenylalanine ammonium lyase, PKS polyketide synthase, NRPS nonribosomal peptide synthase 1 Gerwick 1999 2 Liu et al. 1994 3 Boonprab et al. 2003 4 Cvejic and Rohmer 1999 5 Disch et al. 1998 6 Chikaraishi et al. 2006 7 Schwender et al. 2001 8 Schwender et al. 1997 9 Mayes et al. 1993 10 Shick et al. 1999 11 Richards et al. 2006 12 Bouarab et al. 2004 13 Pelletreau et al., unpublished data 14 Dittman and Weigand 2006 15 Rein and Barrone 1999 Empty columns imply no direct evidence of these enzymes from these systems... 

Solubility and kinetics methods for distinguishing adsorption from surface precipitation suffer from the fundamental weakness of being macroscopic approaches that do not involve a direct examination of the solid phase. Information about the composition of an aqueous solution phase is not sufficient to permit a clear inference of a sorption mechanism because the aqueous solution phase does not determine uniquely the nature of its contiguous solid phases, even at equilibrium (49). Perhaps more important is the fact that adsorption and surface precipitation are essentially molecular concepts on which strictly macroscopic approaches can provide no unambiguous data (12, 21). Molecular concepts can be studied only by molecular methods. 

The voluminous number of publications in this area over the last 10 years have exceeded 10,000, thus attesting to the intensity of effort directed towards applying molecular methods towards investigation of infectious diseases. Many of these investigations have translated into applications for diagnostic use in the clinical laboratory. The reader is referred to selected reviews on the subject (F2, N3, Wl). The availability of assays for the rapid diagnosis of pulmonary tuber-... 

A simple assay for the detection of the malarial parasite Plasmodium falciparum involves saponin lysis of blood sample and membrane filtration followed by amplification of the consensus sequence of eight 21-bp repeats. This procedure has been successfully used in the field (F2). A PCR assay targeting kinetoplast DNA sequences of Leishmania species was also successfully tested in the field (F2). Molecular methods for the detection of toxoplasma gondii and several other parasites have been reviewed (F2). 

A well-known use of molecular methods is in the study of chromosomal translocations. Thus, in Philadelphia chromosome (ph1) positive chronic myelogenous leukemia (CML), the C-abl oncogene on chromosome 9 is translocated to a region on chromosome 22 called the breakpoint cluster region, or bcr. This (t9 22) translocation results in production of an abnormal fusion protein... 

Modern approaches based on the use of molecular techniques presumed to circumvent the need for culturing prokaryotes, fail to provide sufficient and reliable information for estimation of prokaryote diversity. Many properties that make these organisms important members of the living world are amenable to observation only through the study of living cultures. Since current culture techniques do not always satisfy the need of providing a balanced picture of the microflora composition, future developments in the study of bacterial diversity should include improvements in the culture methods to approach as closely as possible the conditions of natural habitats. Molecular methods of microflora analysis have an important role as guides for the isolation of new prokaryotic taxa. 

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