Discriminating cool-water from warm-water carbonates and their diagenetic environments using element geochemistry: the Oligocene Tikorangi Formation (Taranaki Basin) and the dolomite effect

Fields portrayed within bivariate element plots have been used to distinguish between carbonates formed in warm- (tropical) water and cool- (temperate) water depositional settings. Here, element concentrations (Ca, Mg, Sr, Na, Fe, and Mn) have been determined for the carbonate fraction of bulk samples from the late Oligocene Tikorangi Formation, a subsurface, mixed dolomite-calcite, cool-water limestone sequence in Taranaki Basin, New Zealand. While the occurrence of dolomite is rare in New Zealand Cenozoic carbonates, and in cool-water carbonates more generally, the dolomite in the Tikorangi carbonates is shown to have a dramatic effect on the "traditional" positioning of cool-water limestone fields within bivariate element plots. Rare undolomitised, wholly calcitic carbonate samples in the Tikorangi Formation have the following average composition: Mg 2800 ppm; Ca 319 100 ppm; Na 800 ppm; Fe 6300 ppm; Sr 2400 ppm; and Mn 300 ppm. Tikorangi Formation dolomite-rich samples (>15% dolomite) have average values of: Mg 53 400 ppm; Ca 290 400 ppm; Na 4700 ppm; Fe 28 100 ppm; Sr 5400 ppm; and Mn 500 ppm. Element-element plots for dolomite-bearing samples show elevated Mg, Na, and Sr values compared with most other low-Mg calcite New Zealand Cenozoic limestones. The increased trace element contents are directly attributable to the trace element-enriched nature of the burial-derived dolomites, termed here the "dolomite effect". Fe levels in the Tikorangi Formation carbonates far exceed both modern and ancient cool-water and warm-water analogues, while Sr values are also higher than those in modern Tasmanian cool-water carbonates, and approach modern Bahaman warm-water carbonate values. Trace element data used in conjunction with more traditional petrographic data have aided in the diagenetic interpretation of the carbonate-dominated Tikorangi sequence. The geochemical results have been particularly useful for providing more definitive evidence for deep burial dolomitisation of the deposits under the influence of marine-modified pore fluids

Hydrogen bonding in duplex DNA probed by DNP enhanced solid-state NMR N-H bond length measurements

Numerous biological processes and mechanisms depend on details of base pairing and hydrogen bonding in DNA. Hydrogen bonds are challenging to quantify by X-ray crystallography and cryo-EM due to difficulty of visualizing hydrogen atom locations but can be probed with site specificity by NMR spectroscopy in solution and the solid state with the latter particularly suited to large, slowly tumbling DNA complexes. Recently, we showed that low-temperature dynamic nuclear polarization (DNP) enhanced solid-state NMR is a valuable tool for distinguishing Hoogsteen base pairs (bps) from canonical Watson-Crick bps in various DNA systems under native-like conditions. Here, using a model 12-mer DNA duplex containing two central adenine-thymine (A-T) bps in either Watson-Crick or Hoogsteen confirmation, we demonstrate DNP solid-state NMR measurements of thymine N3-H3 bond lengths, which are sensitive to details of N-H···N hydrogen bonding and permit hydrogen bonds for the two bp conformers to be systematically compared within the same DNA sequence context. For this DNA duplex, effectively identical TN3-H3 bond lengths of 1.055 ± 0.011 Å and 1.060 ± 0.011 Å were found for Watson-Crick A-T and Hoogsteen A (syn)-T base pairs, respectively, relative to a reference amide bond length of 1.015 ± 0.010 Å determined for N-acetyl-valine under comparable experimental conditions. Considering that prior quantum chemical calculations which account for zero-point motions predict a somewhat longer effective peptide N-H bond length of 1.041 Å, in agreement with solution and solid-state NMR studies of peptides and proteins at ambient temperature, to facilitate direct comparisons with these earlier studies TN3-H3 bond lengths for the DNA samples can be readily scaled appropriately to yield 1.083 Å and 1.087 Å for Watson-Crick A-T and Hoogsteen A (syn)-T bps, respectively, relative to the 1.041 Å reference peptide N-H bond length. Remarkably, in the context of the model DNA duplex, these results indicate that there are no significant differences in N-H···N A-T hydrogen bonds between Watson-Crick and Hoogsteen bp conformers. More generally, high precision measurements of N-H bond lengths by low-temperature DNP solid-state NMR based methods are expected to facilitate detailed comparative analysis of hydrogen bonding for a range of DNA complexes and base pairing environments

Visualizing spatially correlated dynamics that directs RNA conformational transitions

RNAs fold into three- dimensional ( 3D) structures that subsequently undergo large, functionally important, conformational transitions in response to a variety of cellular signals(1-3). RNA structures are believed to encode spatially tuned flexibility that can direct transitions along specific conformational pathways(4,5). However, this hypothesis has proved difficult to examine directly because atomic movements in complex biomolecules cannot be visualized in 3D by using current experimental methods. Here we report the successful implementation of a strategy using NMR that has allowed us to visualize, with complete 3D rotational sensitivity, the dynamics between two RNA helices that are linked by a functionally important trinucleotide bulge over timescales extending up to milliseconds. The key to our approach is to anchor NMR frames of reference onto each helix and thereby directly measure their dynamics, one relative to the other, using 'relativistic' sets of residual dipolar couplings ( RDCs)(6,7). Using this approach, we uncovered super- large amplitude helix motions that trace out a surprisingly structured and spatially correlated 3D dynamic trajectory. The two helices twist around their individual axes by approximately 536 and 1106 in a highly correlated manner ( R = 0.97) while simultaneously ( R = 0.81 - 0.92) bending by about 94 degrees. Remarkably, the 3D dynamic trajectory is dotted at various positions by seven distinct ligand- bound conformations of the RNA. Thus even partly unstructured RNAs can undergo structured dynamics that directs ligand- induced transitions along specific predefined conformational pathways.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62506/1/nature06389.pd

Design Principles for Ligand-Sensing, Conformation-Switching Ribozymes

Nucleic acid sensor elements are proving increasingly useful in biotechnology and biomedical applications. A number of ligand-sensing, conformational-switching ribozymes (also known as allosteric ribozymes or aptazymes) have been generated by some combination of directed evolution or rational design. Such sensor elements typically fuse a molecular recognition domain (aptamer) with a catalytic signal generator (ribozyme). Although the rational design of aptazymes has begun to be explored, the relationships between the thermodynamics of aptazyme conformational changes and aptazyme performance in vitro and in vivo have not been examined in a quantitative framework. We have therefore developed a quantitative and predictive model for aptazymes as biosensors in vitro and as riboswitches in vivo. In the process, we have identified key relationships (or dimensionless parameters) that dictate aptazyme performance, and in consequence, established equations for precisely engineering aptazyme function. In particular, our analysis quantifies the intrinsic trade-off between ligand sensitivity and the dynamic range of activity. We were also able to determine how in vivo parameters, such as mRNA degradation rates, impact the design and function of aptazymes when used as riboswitches. Using this theoretical framework we were able to achieve quantitative agreement between our models and published data. In consequence, we are able to suggest experimental guidelines for quantitatively predicting the performance of aptazyme-based riboswitches. By identifying factors that limit the performance of previously published systems we were able to generate immediately testable hypotheses for their improvement. The robust theoretical framework and identified optimization parameters should now enable the precision design of aptazymes for biotechnological and clinical applications

Lattice QCD Simulations in External Background Fields

We discuss recent results and future prospects regarding the investigation, by lattice simulations, of the non-perturbative properties of QCD and of its phase diagram in presence of magnetic or chromomagnetic background fields. After a brief introduction to the formulation of lattice QCD in presence of external fields, we focus on studies regarding the effects of external fields on chiral symmetry breaking, on its restoration at finite temperature and on deconfinement. We conclude with a few comments regarding the effects of electromagnetic background fields on gluodynamics.Comment: 31 pages, 10 figures, minor changes and references added. To appear in Lect. Notes Phys. "Strongly interacting matter in magnetic fields" (Springer), edited by D. Kharzeev, K. Landsteiner, A. Schmitt, H.-U. Ye

Yield of soybean genotypes identified through GGE biplot and path analysis.

Genotype x environment (GxE) interaction is an important source of variation in soybean yield, which can significantly influence selection in breeding programs. This study aimed to select superior soybean genotypes for performance and yield stability, from data from multienvironment trials (METs), through GGE biplot analysis that combines the main effects of the genotype (G) plus the genotype-by-environment (G×E) interaction. As well as, through path analysis, determine the direct and indirect influences of yield components on soybean grain yield, as a genotype selection strategy

Fluorescent RNA cytosine analogue - an internal probe for detailed structure and dynamics investigations

The bright fluorescent cytosine analogue tCO stands out among fluorescent bases due to its virtually unquenched fluorescence emission in duplex DNA. However, like most reported base analogues, it has not been thoroughly characterized in RNA. We here report on the first synthesis and RNA-incorporation of tCO, and characterize its base-mimicking and fluorescence properties in RNA. As in DNA, we find a high quantum yield inside RNA duplexes (<?F> = 0.22) that is virtually unaffected by the neighbouring bases (?F = 0.20-0.25), resulting in an average brightness of 1900 M-1 cm-1. The average fluorescence lifetime in RNA duplexes is 4.3 ns and generally two lifetimes are required to fit the exponential decays. Fluorescence properties in ssRNA are defined by a small increase in average quantum yield (<?F > = 0.24) compared to dsRNA, with a broader distribution (?F = 0.17-0.34) and slightly shorter average lifetimes. Using circular dichroism, we find that the tCO-modified RNA duplexes form regular A-form helices and in UV-melting experiments the stability of the duplexes is only slightly higher than that of the corresponding natural RNA (<?T m> = + 2.3 °C). These properties make tCO a highly interesting fluorescent RNA base analogue for detailed FRET-based structural measurements, as a bright internal label in microscopy, and for fluorescence anisotropy measurements of RNA dynamics

Smoking and drinking in relation to oral potentially malignant disorders in Puerto Rico: a case-control study

<p>Abstract</p> <p>Background</p> <p>Oral cancer incidence is high on the Island of Puerto Rico (PR), particularly among males. As part of a larger study conducted in PR, we evaluated smoking and drinking as risk factors for oral potentially malignant disorders (OPMDs).</p> <p>Methods</p> <p>Persons diagnosed with either an OPMD (n = 86) [oral epithelial dysplasia (OED), oral hyperkeratosis/epithelial hyperplasia without OED] or a benign oral tissue condition (n = 155) were identified through PR pathology laboratories. Subjects were interviewed using a standardized, structured questionnaire that obtained information, including detailed histories of smoking and drinking. Odds ratios (ORs) for smoking and drinking in relation to having an OPMD, relative to persons with a benign oral tissue condition, were obtained using logistic regression and adjusted for age, gender, education, fruit/vegetable intake and smoking or drinking.</p> <p>Results</p> <p>For persons with an OPMD and relative to individuals with a benign oral tissue condition, the adjusted OR for current smoking was 4.32 (95% CI: 1.99-9.38), while for former smokers, the OR_adjwas 1.47 (95% CI: 0.67-3.21), each OR_adjrelative to never smokers. With regard to drinking, no adjusted ORs approached statistical significance, and few point estimates exceeded 1.0, whether consumption was defined in terms of ever, current, level (drinks/week), or beverage type.</p> <p>Conclusions</p> <p>In this study, conducted in Puerto Rico, current smoking was a substantial risk factor for OPMDs while former smokers had a considerably reduced risk compared to current smokers. There was little evidence suggesting that alcohol consumption was positively associated with OPMD risk.</p