Rapid, solid-phase based automated analysis of chromatin structure and transcription factor occupancy in living eukaryotic cells

Transcription factors, chromatin components and chromatin modification activities are involved in many diseases including cancer. However, the means by which alterations in these factors influence the epigenotype of specific cell types is poorly understood. One problem that limits progress is that regulatory regions of eukaryotic genes sometimes extend over large regions of DNA. To improve chromatin structure–function analysis over such large regions, we have developed an automated, relatively simple procedure that uses magnetic beads and a capillary sequencer for ligation-mediated-PCR (LM-PCR). We show that the procedure can be used for the rapid examination of chromatin fine-structure, nucleosome positioning as well as changes in transcription factor binding-site occupancy during cellular differentiation

Estimating Discharge in Low-Order Rivers With High-Resolution Aerial Imagery

Remote sensing of river discharge promises to augment in situ gauging stations, but the majority of research in this field focuses on large rivers (\u3e50 m wide). We present a method for estimating volumetric river discharge in low-order (wide) rivers from remotely sensed data by coupling high-resolution imagery with one-dimensional hydraulic modeling at so-called virtual gauging stations. These locations were identified as locations where the river contracted under low flows, exposing a substantial portion of the river bed. Topography of the exposed river bed was photogrammetrically extracted from high-resolution aerial imagery while the geometry of the remaining inundated portion of the channel was approximated based on adjacent bank topography and maximum depth assumptions. Full channel bathymetry was used to create hydraulic models that encompassed virtual gauging stations. Discharge for each aerial survey was estimated with the hydraulic model by matching modeled and remotely sensed wetted widths. Based on these results, synthetic width-discharge rating curves were produced for each virtual gauging station. In situ observations were used to determine the accuracy of wetted widths extracted from imagery (mean error 0.36 m), extracted bathymetry (mean vertical RMSE 0.23 m), and discharge (mean percent error 7% with a standard deviation of 6%). Sensitivity analyses were conducted to determine the influence of inundated channel bathymetry and roughness parameters on estimated discharge. Comparison of synthetic rating curves produced through sensitivity analyses show that reasonable ranges of parameter values result in mean percent errors in predicted discharges of 12%–27%

Proteins to Order Use of Synthetic DNA to Generate Site-Specific Mutations

The ability to cause specific changes in the amino acid sequences of proteins would greatly advance studies on the influence of protein structure on biochemical function. If the desired changes can once be made in the nucleic acid which encodes the protein, one can use cloning in an appropriate microorganism to produce essentially limitless quantities of the mutant protein. We describe here the application of oligonucleotide-directed site-specific mutagenesis to accomplish this objective for the enzyme B-lactamase, the gene for which is contained in the plasmid pBR322. The method uses a procedure to screen for mutant clones which depends on the DNA in the various colonies and not on the properties of the mutant protein; the method can, therefore, be widely applied and does not require, in each separate case, the development of a screening procedure which depends on some phenotypic difference between mutant and wild-type protein

Possible scale invariant linear magnetoresistance in pyrochlore iridates Bi2Ir2O7

We report the observation of a linear magnetoresistance in single crystals and epitaxial thin films of the pyrochlore iridate Bi2Ir2O7. The linear magnetoresistance is positive and isotropic at low temperatures, without any sign of saturation up to 35 T. As temperature increases, the linear field dependence gradually evolves to a quadratic field dependence. The temperature and field dependence of magnetoresistance of Bi2Ir2O7 bears strikingly resemblance to the scale invariant magnetoresistance observed in the strange metal phase in high Tc cuprates. However, the residual resistivity of Bi2Ir2O7 is more than two orders of magnitude higher than the curpates. Our results suggest that the correlation between linear magnetoresistance and quantum fluctuations may exist beyond high temperature superconductors

A proposed prioritization system for the management of invasive alien plants in South Africa

Every country has weed species whose presence conflicts in some way with human management objectives and needs. Resources for research and control are limited, so priority should be given to species that are the biggest problem. The prioritization system described in this article was designed to assess objectively research and control priorities of invasive alien plants at a national scale in South Africa. The evaluation consists of seventeen criteria, grouped into five modules, that assess invasiveness, spatial characteristics, potential impact, potential for control, and conflicts of interest for each plant species under consideration. Total prioritization scores, calculated from criterion and module scores, were used to assess a species' priority. Prioritization scores were calculated by combining independent assessments provided by several experts, thus increasing the reliability of the rankings. The total confidence score, a separate index, indicates the reliability and availability of data used to make an assessment. Candidate species for evaluation were identified and assessed by several experts using the prioritization system. The final ranking was made by combining two separate indices, the total prioritization score and the total confidence score. This approach integrates the plant's perceived priority with an index of data reliability. Of the 61 species assessed, those with the highest ranks (Lantana camara, Chromolaena odorata and Opuntia ficus-indica) had high prioritization and high confidence scores, and are thus of most concern. Those species with the lowest ranks, for example, Harrisia martinii, Opuntia spinulifera and Opuntia exaltata, had low prioritization scores and high confidence scores, and thus are of least concern. Our approach to ranking weeds offers several advantages over existing systems because it is designed for multiple assessors based on the Delphi decision-making technique, the criteria contribute equally to the total score, and the system can accommodate incomplete data on a species. Although the choice of criteria may be criticized and the system has certain limitations, it appears to have delivered credible results