| 1. |
- Ali, Tara, 1980-, et al.
(författare)
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Liquid extraction of low molecular mass organic acids and hydroxamate siderophores from boreal forest soil
- 2011
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Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 43:12, s. 2417-2422
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Tidskriftsartikel (refereegranskat)abstract
- Low molecular mass organic acids (LMMOAs) and hydroxamate siderophores (HS) are molecules secreted by microbes and have previously been found in soil solution and in cultures. Mycorrhizal fungi are suggested to be involved in the nutrient uptake processes of trees and weathering of minerals. In this study soil samples taken from the O and E horizons of a podzol were extracted with 10 mM potassium phosphate buffer at pH 7.2. Variable parameters included addition of methanol to the extraction buffer and the use of ultrasonication or rotary shaking during extraction. LMMOAs and HS content of the soil extracts were determined. Analysis of soil extracts were carried out by liquid chromatography mass spectrometry (LC-MS) and the extraction results compared to results for soil solution samples obtained by centrifugation of the soils sampled. The extraction yields were significantly increased by addition of methanol to the extraction buffer, especially for the O horizon samples. Rotary shaking of the samples for 90 min gave slightly higher yields than ultrasonication for 15 min but the reduction in extraction time makes ultrasonication an attractive option. Of the HSs determined, ferricrocin was found in all samples. Optimal extraction conditions showed citric acid and isocitric acid to be the most abundant organic acids in the O and E horizons, respectively.
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| 2. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 3. |
- Zaccheus, Mona V., et al.
(författare)
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The Epitopic and Structural Characterization of Brucella suis Biovar 2 O-Polysaccharide Demonstrates the Existence of a New M-Negative C-Negative Smooth Brucella Serovar
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:1, s. e53941-
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Tidskriftsartikel (refereegranskat)abstract
- The brucellae are Gram-negative bacteria that cause an important zoonosis. Studies with the main Brucella species have shown that the O-antigens of the Brucella smooth lipopolysaccharide are alpha-(1 -> 2) and alpha-(1 -> 3)-linked N-formyl-perosamine polysaccharides that carry M, A and C (A = M, A>M and AA) and M specificities. However, the biovar 2 O-antigen bound monoclonal antibodies to the Brucella A epitope, and to the C/Y epitope shared by brucellae and Yersinia enterocolitica O:9, a bacterium that carries an N-formyl-perosamine O-antigen in exclusively alpha-(1 -> 2)-linkages. By C-13 NMR spectroscopy, B. suis biovar 1 but not B. suis biovar 2 or Y.enterocolitica O:9 polysaccharide showed the signal characteristic of alpha-(1 -> 3)-linked N-formyl-perosamine, indicating that biovar 2 may altogether lack this linkage. Taken together, the NMR spectroscopy and monoclonal antibody analyses strongly suggest a role for alpha-(1 -> 3)-linked N-formyl-perosamine in the C (A = M) and C (M>A) epitopes. Moreover, they indicate that B. suis biovar 2 O-antigen lacks some lipopolysaccharide epitopes previously thought to be present in all smooth brucellae, thus representing a new brucella serovar that is M-negative, C-negative. Serologically and structurally this new serovar is more similar to Y. enterocolitica O:9 than to other brucellae.
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