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author:("farjo, A")
1.  Longitudinal-relaxation-enhanced NMR experiments for the study of nucleic acids in solution 
Atomic-resolution information on the structure and dynamics of nucleic acids is essential for a better understanding of the mechanistic basis of many cellular processes. NMR spectroscopy is a powerful method for studying the structure and dynamics of nucleic acids; however, solution NMR studies are currently limited to relatively small nucleic acids at high concentrations. Thus, technological and methodological improvements that increase the experimental sensitivity and spectral resolution of NMR spectroscopy are required for studies of larger nucleic acids or protein-nucleic acid complexes. Here we introduce a series of imino-proton-detected NMR experiments that yield over a 2-fold increase in sensitivity compared to conventional pulse schemes. These methods can be applied to the detection of base pair interactions, RNA-ligand titration experiments, measurement of residual dipolar 15N-1H couplings, as well as direct measurements of conformational transitions. These NMR experiments employ longitudinal spin relaxation enhancement techniques that have proven useful in protein NMR spectroscopy. The performance of these new experiments is demonstrated for a 10 kDa TAR-TAR*GA RNA kissing complex and a 26 kDa tRNA.
doi:10.1021/ja901633y
PMCID: PMC2846706  PMID: 19485365
RNA; DNA; structure; dynamics; TROSY; SOFAST; hydrogen bond; longitudinal-relaxation enhancement; molecular kinetics
2.  Measuring the fate of plant diversity: towards a foundation for future monitoring and opportunities for urgent action 
Vascular plants are often considered to be among the better known large groups of organisms, but gaps in the available baseline data are extensive, and recent estimates of total known (described) seed plant species range from 200 000 to 422 000. Of these, global assessments of conservation status using International Union for the Conservation of Nature (IUCN) categories and criteria are available for only approximately 10 000 species. In response to recommendations from the Conference of the Parties to the Convention on Biological Diversity to develop biodiversity indicators based on changes in the status of threatened species, and trends in the abundance and distribution of selected species, we examine how existing data, in combination with limited new data collection, can be used to maximum effect. We argue that future work should produce Red List Indices based on a representative subset of plant species so that the limited resources currently available are directed towards redressing taxonomic and geographical biases apparent in existing datasets. Sampling the data held in the world's major herbaria, in combination with Geographical Information Systems techniques, can produce preliminary conservation assessments and help to direct selective survey work using existing field networks to verify distributions and gather population data. Such data can also be used to backcast threats and potential distributions through time. We outline an approach that could result in: (i) preliminary assessments of the conservation status of tens of thousands of species not previously assessed, (ii) significant enhancements in the coverage and representation of plant species on the IUCN Red List, and (iii) repeat and/or retrospective assessments for a significant proportion of these. This would result in more robust Sampled Red List Indices that can be defended as more representative of plant diversity as a whole; and eventually, comprehensive assessments at species level for one or more major families of angiosperms. The combined results would allow scientifically defensible generalizations about the current status of plant diversity by 2010 as well as tentative comments on trends. Together with other efforts already underway, this approach would establish a firmer basis for ongoing monitoring of the status of plant diversity beyond 2010 and a basis for comparison with the trend data available for vertebrates.
doi:10.1098/rstb.2004.1596
PMCID: PMC1569457  PMID: 15814350
global biodiversity; species richness; conservation assessments; extinction risk; IUCN Red List; Living Planet Index
3.  Non-invasive diagnosis and assessment of tricuspid regurgitation and stenosis using one and two dimensional echo-pulsed Doppler. 
British Heart Journal  1982;47(6):596-605.
Twenty normal subjects and 82 patients with valvular heart disease, whose lesions were independently assessed either by cardiac catheterisation and/or at operation, were studied using the pulsed Doppler technique combined with either one or two dimensional echocardiography. Of these, 41 patients had tricuspid lesions, including 40 with regurgitation and nine with stenosis. The tricuspid analogue flow velocity trace and the Doppler frequency spectrum (time interval histogram) were recorded. Characteristic differences were found between the records from subjects with and without tricuspid lesions. In subjects with tricuspid regurgitation there was a systolic negative wave on the analogue velocity display and broadening of the time interval histogram. In subjects with tricuspid stenosis there was an abnormal pattern, and significantly increased duration of the diastolic wave on the analogue velocity trace, again with broadening of the time interval histogram. Sensitivity and specificity ranged between 85 and 95%. The calculated ratio between the measured amplitudes of the systolic and diastolic waves correlated well with independently performed grading of the regurgitation on a three point scale in 85% of cases. Grading of the severity of tricuspid stenosis on a three point scale based on studies of the diastolic Doppler velocity anomalies was the same in 85% of cases as the grading based on established invasive techniques. The addition of two dimensional echocardiography to the pulsed Doppler technique increased the sensitivity for mild lesions.
Images
PMCID: PMC481187  PMID: 7082507

Results 1-3 (3)