DNA Free Energy-Based Promoter Prediction and Comparative Analysis of Arabidopsis and Rice Genomes

The cis-regulatory regions on DNA serve as binding sites for proteins such as transcription factors and RNA polymerase. The combinatorial interaction of these proteins plays a crucial role in transcription initiation, which is an important point of control in the regulation of gene expression. We present here an analysis of the performance of an in silico method for predicting cis-regulatory regions in the plant genomes of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) on the basis of free energy of DNA melting. For protein-coding genes, we achieve recall and precision of 96% and 42% for Arabidopsis and 97% and 31% for rice, respectively. For noncoding RNA genes, the program gives recall and precision of 94% and 75% for Arabidopsis and 95% and 90% for rice, respectively. Moreover, 96% of the false-positive predictions were located in noncoding regions of primary transcripts, out of which 20% were found in the first intron alone, indicating possible regulatory roles. The predictions for orthologous genes from the two genomes showed a good correlation with respect to prediction scores and promoter organization. Comparison of our results with an existing program for promoter prediction in plant genomes indicates that our method shows improved prediction capability.

Combining indentation and diffusion couple techniques for combinatorial discovery of high temperature shape memory alloys

We demonstrate the possibility of accelerated identification of potential compositions for high-temperature shape memory alloys (SMAs) through a combinatorial material synthesis and analysis approach, wherein we employ the combination of diffusion couple and indentation techniques. The former was utilized to generate smooth and compositionally graded inter-diffusion zones (IDZs) in the Ni-Ti-Pd ternary alloy system of varying IDZ thickness, depending on the annealing time at high temperature. The IDZs thus produced were then impressed with an indenter with a spherical tip so as to inscribe a predetermined indentation strain. Subsequent annealing of the indented samples at various elevated temperatures, T-a, ranging between 150 and 550 degrees C allows for partial to full relaxation of the strain imposed due to the shape memory effect. If T-a is above the austenite finish temperature, A(f), the relaxation will be complete. By measuring the depth recovery, which serves as a proxy for the shape recovery characteristic of the SMA, a three-dimensional map in the recovery temperature composition space is constructed. A comparison of the published Af data for different compositions with the Ta data shows good agreement when the depth recovery is between 70% and 80%, indicating that the methodology proposed in this paper can be utilized for the identification of promising compositions. Advantages and further possibilities of this methodology are discussed.

Combinatorial Exploration of the Structural Landscape of Acid-Pyridine Cocrystals

The structural landscape of acid-pyridine cocrystals is explored by adopting a combinatorial matrix method with 4-substituted benzoic acids and 4-substituted pyridines. The choice of the system restricts the primary synthon to the robust acid-pyridine entity. This methodology accordingly provides hints toward the formation of secondary synthons. The pK(a) rule is validated in the landscape by taking all components of the matrix together and exploring it as a whole. Along with the global features, the exploration of landscapes reveals some local features. Apart from the identification of secondary synthons, it also sheds light on the propensity of hydration in cocrystals, synthon competition, and certain topological similarities. The method described here combines two approaches, namely, database analysis and high throughput crystallography, to extract more information with minimal extra experimental effort.