Application of time-dependent density functional theory to optical activity

As part of a general study of the time-dependent local density approximation (TDLDA), we here report calculations of optical activity of chiral molecules. The theory automatically satisfies sum rules and the Kramers-Kronig relation between circular dichroism and optical rotatory power. We find that the theory describes the measured circular dichroism of the lowest states in methyloxirane with an accuracy of about a factor of two. In the chiral fullerene C_76 the TDLDA provides a consistent description of the optical absorption spectrum, the circular dichroism spectrum, and the optical rotatory power, except for an overall shift of the theoretical spectrum.Comment: 17 pages and 13 PostScript figure

Components of resistance to sorghum shoot fly, Atherigona soccata

Sorghum shoot fly, Atherigona soccata is one of the major constraints in sorghum production, and host plant resistance is one of the components to control sorghum shoot fly. Thirty sorghum genotypes were evaluated for different mechanisms of resistance and morphological and agronomic traits during the rainy and postrainy seasons. The sorghum genotypes, Maulee, Phule Anuradha, M 35-1, CSV 18R, IS 2312, Giddi Maldandi, and RVRT 3 suffered lower shoot fly damage, and also exhibited high grain yield potential during the postrainy season. ICSB 433, ICSV 700, ICSV 25019, ICSV 25022, ICSV 25026, ICSV 25039, PS 35805, Akola Kranti, and IS 18551 exhibited antixenosis for oviposition and antibiosis against sorghum shoot fly, A. soccata. Leaf glossiness, plant vigor, leafsheath pigmentation and trichomes were associated with resistance/susceptibility to shoot fly. Path coefficient analysis indicated that direct effects and correlation coefficients of leaf glossiness, plant vigor, plant height, plant color and trichomes were in the same direction, suggesting that these traits can be used to select sorghum genotypes for resistance to shoot fly. Principal co-ordinate analysis based on shoot fly resistance traits and morphological traits placed the test genotypes into different groups. The genotypes placed in different groups can be used to increase the levels and broaden the genetic base of resistance to shoot fly. The environmental coefficient of variation and phenotypic coefficient of variation for shoot fly resistance and morphological traits were quite high, indicating season specific expression of resistance to sorghum shoot fly. High broadsense heritability, genetic advance and genotypic coefficient of variation suggested the predominance of additive nature of genes controlling shoot fly resistance, suggesting that pedigree breeding can be used to transfer shoot fly resistance into high yielding cultivars. This information will be useful for developing shoot fly-resistant high yielding cultivars for sustainable crop production

Caipirini: using gene sets to rank literature

<p>Abstract</p> <p>Background</p> <p>Keeping up-to-date with bioscience literature is becoming increasingly challenging. Several recent methods help meet this challenge by allowing literature search to be launched based on lists of abstracts that the user judges to be 'interesting'. Some methods go further by allowing the user to provide a second input set of 'uninteresting' abstracts; these two input sets are then used to search and rank literature by relevance. In this work we present the service 'Caipirini' (<url>http://caipirini.org</url>) that also allows two input sets, but takes the novel approach of allowing ranking of literature based on one or more sets of genes.</p> <p>Results</p> <p>To evaluate the usefulness of Caipirini, we used two test cases, one related to the human cell cycle, and a second related to disease defense mechanisms in <it>Arabidopsis thaliana</it>. In both cases, the new method achieved high precision in finding literature related to the biological mechanisms underlying the input data sets.</p> <p>Conclusions</p> <p>To our knowledge Caipirini is the first service enabling literature search directly based on biological relevance to gene sets; thus, Caipirini gives the research community a new way to unlock hidden knowledge from gene sets derived via high-throughput experiments.</p

GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique

<p>Abstract</p> <p>Background</p> <p>Synthesis of data from published human genetic association studies is a critical step in the translation of human genome discoveries into health applications. Although genetic association studies account for a substantial proportion of the abstracts in PubMed, identifying them with standard queries is not always accurate or efficient. Further automating the literature-screening process can reduce the burden of a labor-intensive and time-consuming traditional literature search. The Support Vector Machine (SVM), a well-established machine learning technique, has been successful in classifying text, including biomedical literature. The GAPscreener, a free SVM-based software tool, can be used to assist in screening PubMed abstracts for human genetic association studies.</p> <p>Results</p> <p>The data source for this research was the HuGE Navigator, formerly known as the HuGE Pub Lit database. Weighted SVM feature selection based on a keyword list obtained by the two-way z score method demonstrated the best screening performance, achieving 97.5% recall, 98.3% specificity and 31.9% precision in performance testing. Compared with the traditional screening process based on a complex PubMed query, the SVM tool reduced by about 90% the number of abstracts requiring individual review by the database curator. The tool also ascertained 47 articles that were missed by the traditional literature screening process during the 4-week test period. We examined the literature on genetic associations with preterm birth as an example. Compared with the traditional, manual process, the GAPscreener both reduced effort and improved accuracy.</p> <p>Conclusion</p> <p>GAPscreener is the first free SVM-based application available for screening the human genetic association literature in PubMed with high recall and specificity. The user-friendly graphical user interface makes this a practical, stand-alone application. The software can be downloaded at no charge.</p

Exome reanalysis and proteomic profiling identified TRIP4 as a novel cause of cerebellar hypoplasia and spinal muscular atrophy (PCH1)

TRIP4 is one of the subunits of the transcriptional coregulator ASC-1, a ribonucleoprotein complex that participates in transcriptional coactivation and RNA processing events. Recessive variants in the TRIP4 gene have been associated with spinal muscular atrophy with bone fractures as well as a severe form of congenital muscular dystrophy. Here we present the diagnostic journey of a patient with cerebellar hypoplasia and spinal muscular atrophy (PCH1) and congenital bone fractures. Initial exome sequencing analysis revealed no candidate variants. Reanalysis of the exome data by inclusion in the Solve-RD project resulted in the identification of a homozygous stop-gain variant in the TRIP4 gene, previously reported as disease-causing. This highlights the importance of analysis reiteration and improved and updated bioinformatic pipelines. Proteomic profile of the patient’s fibroblasts showed altered RNA-processing and impaired exosome activity supporting the pathogenicity of the detected variant. In addition, we identified a novel genetic form of PCH1, further strengthening the link of this characteristic phenotype with altered RNA metabolism

Gene Expression Profiles of the NCI-60 Human Tumor Cell Lines Define Molecular Interaction Networks Governing Cell Migration Processes

Although there is extensive information on gene expression and molecular interactions in various cell types, integrating those data in a functionally coherent manner remains challenging. This study explores the premise that genes whose expression at the mRNA level is correlated over diverse cell lines are likely to function together in a network of molecular interactions. We previously derived expression-correlated gene clusters from the database of the NCI-60 human tumor cell lines and associated each cluster with function categories of the Gene Ontology (GO) database. From a cluster rich in genes associated with GO categories related to cell migration, we extracted 15 genes that were highly cross-correlated; prominent among them were RRAS, AXL, ADAM9, FN14, and integrin-beta1. We then used those 15 genes as bait to identify other correlated genes in the NCI-60 database. A survey of current literature disclosed, not only that many of the expression-correlated genes engaged in molecular interactions related to migration, invasion, and metastasis, but that highly cross-correlated subsets of those genes engaged in specific cell migration processes. We assembled this information in molecular interaction maps (MIMs) that depict networks governing 3 cell migration processes: degradation of extracellular matrix, production of transient focal complexes at the leading edge of the cell, and retraction of the rear part of the cell. Also depicted are interactions controlling the release and effects of calcium ions, which may regulate migration in a spaciotemporal manner in the cell. The MIMs and associated text comprise a detailed and integrated summary of what is currently known or surmised about the role of the expression cross-correlated genes in molecular networks governing those processes

Chemical Behavior and Reaction Kinetics of Sulfur and Nitrogen Half-Mustard and Iprit Carbonate Analogues

Sulfur and nitrogen mustards are very toxic, yet versatile organic molecules with numerous applications. Herein, we report on a synthesis of a new class of green compounds, i.e., half-mustard and iprit carbonates, that result in new, unexplored, and safe molecules. Their chemical behavior with several nucleophiles and their reaction kinetics have been investigated