Investigations into the molecular effects of single nucleotide polymorphism

Objectives: DNA sequences are very rich in short repeats and their pattern can be altered by point mutations. We wanted to investigate the effect of single nucleotide polymorphism (SNP) on the pattern of short DNA repeats and its biological consequences. Methods: Analysis of the pattern of short DNA repeats of the Thy-1 sequence with and without SNP. Searching for DNA-binding factors in any region of significance. Results: Comparing the pattern of short repeats in the Thy-1 gene sequences of Turkish patients with ataxia telangiectasia (AT) with the `wild type' sequence from the DNA database, we identified a missing 8-bp repeat element due to an SNP in position 1271 (intron II) in AT-DNA sequences. Only the mutated sequence had the potential for the formation of a stem loop in DNA or pre-mRNA. In super-shift experiments we found that DNA oligomers covering the area of this SNP formed a complex with proteins amongst which we identified the proliferating cell nuclear antigen (PCNA) protein. Conclusion: SNPs have the potential to alter DNA or pre-mRNA conformation. Although no SNP-depeding formation of the DNA-protein complex was evident, future investigations could reveal differential molecular mechanisms of cellular regulation. Copyright (C) 2001 S. Karger AG, Basel

Recent Changes in Chinese and India's Agriculture and Implications on Global Trade of Agricultural Commodities

The objective of this study is to evaluate the changes in import and export demand in China and India on the United States and global agriculture in 2020. A spatial equilibrium model is developed to optimize production and trade in China, India, and other major importing and exporting regions in the world. This research focuses on four primary crops: wheat, corn, rice and soybeans. In the model, China and India are divided into 31 and 14 regions, respectively. The model also includes five exporting countries and ten importing countries/regions. The results indicate that India will be able to stay largely self-sufficient in 2020 and China will increase its soybean and corn imports to meet rising domestic demand. The research also gives perspectives on production and trade in the United States and other major exporting and importing countries.Agribusiness,

Could the Pioneer anomaly have a gravitational origin?

If the Pioneer anomaly has a gravitational origin, it would, according to the equivalence principle, distort the motions of the planets in the Solar System. Since no anomalous motion of the planets has been detected, it is generally believed that the Pioneer anomaly can not originate from a gravitational source in the Solar System. However, this conclusion becomes less obvious when considering models that either imply modifications to gravity at long range or gravitational sources localized to the outer Solar System, given the uncertainty in the orbital parameters of the outer planets. Following the general assumption that the Pioneer spacecraft move geodesically in a spherically symmetric spacetime metric, we derive the metric disturbance that is needed in order to account for the Pioneer anomaly. We then analyze the residual effects on the astronomical observables of the three outer planets that would arise from this metric disturbance, given an arbitrary metric theory of gravity. Providing a method for comparing the computed residuals with actual residuals, our results imply that the presence of a perturbation to the gravitational field necessary to induce the Pioneer anomaly is in conflict with available data for the planets Uranus and Pluto, but not for Neptune. We therefore conclude that the motion of the Pioneer spacecraft must be non-geodesic. Since our results are model independent within the class of metric theories of gravity, they can be applied to rule out any model of the Pioneer anomaly that implies that the Pioneer spacecraft move geodesically in a perturbed spacetime metric, regardless of the origin of this metric disturbance.Comment: 16 pages, 6 figures. Rev. 3: Major revision. Accepted for publication in Phys. Rev. D. Rev. 4: Added two reference

Robustifying trial-derived optimal treatment rules for a target population

Treatment rules based on individual patient characteristics that are easy to interpret and disseminate are important in clinical practice. Properly planned and conducted randomized clinical trials are used to construct individualized treatment rules. However, it is often a concern that trial participants lack representativeness, so it limits the applicability of the derived rules to a target population. In this work, we use data from a single trial study to propose a two-stage procedure to derive a robust and parsimonious rule to maximize the benefit in the target population. The procedure allows a wide range of possible covariate distributions in the target population, with minimal assumptions on the first two moments of the covariate distribution. The practical utility and favorable performance of the methodology are demonstrated using extensive simulations and a real data application

Nonlinear electrodynamics and the Pioneer 10/11 spacecraft anomaly

The occurrence of the phenomenon known as photon acceleration is a natural prediction of nonlinear electrodynamics (NLED). This would appear as an anomalous frequency shift in any modeling of the electromagnetic field that only takes into account the classical Maxwell theory. Thus, it is tempting to address the unresolved anomalous, steady; but time-dependent, blueshift of the Pioneer 10/11 spacecrafts within the framework of NLED. Here we show that astrophysical data on the strength of the magnetic field in both the Galaxy and the local (super)cluster of galaxies support the view on the major Pioneer anomaly as a consequence of the phenomenon of photon acceleration. If confirmed, through further observations or lab experiments, the reality of this phenomenon should prompt to take it into account in any forthcoming research on both cosmological evolution and origin and dynamical effects of primordial magnetic fields, whose seeds are estimated to be very weak.Comment: Final version accepted for publication in Europhysics Letters, uses EPL style, 7 page

Social and ethical checkpoints for bottom-up synthetic biology, or protocells

An alternative to creating novel organisms through the traditional “top-down” approach to synthetic biology involves creating them from the “bottom up” by assembling them from non-living components; the products of this approach are called “protocells.” In this paper we describe how bottom-up and top-down synthetic biology differ, review the current state of protocell research and development, and examine the unique ethical, social, and regulatory issues raised by bottom-up synthetic biology. Protocells have not yet been developed, but many expect this to happen within the next five to ten years. Accordingly, we identify six key checkpoints in protocell development at which particular attention should be given to specific ethical, social and regulatory issues concerning bottom-up synthetic biology, and make ten recommendations for responsible protocell science that are tied to the achievement of these checkpoints