Gene function classification using NCI-60 cell line gene expression profiles

Gene expression patterns from NCI's panel of 60 cell lines were used to train a Neural Network model for classifying genes to pathways. The model assigns probabilities to each gene for each of the 21 modeled pathways assigned by the Kyoto Encyclopedia of Genes and Genomes. Cross-validation of the model showed that 10 of the 21 pathways exhibited good performance in statistical significance and accuracy. The model was designed to output gene probabilities that could be screened for higher probabilities resulting in higher confidence in classification though yielding fewer genes per pathway. The model was deployed on 5798 genes and our approach allowed us to ascertain the most relevant genes above an estimated background. Eight pathways were identified with both good cross-validation and significant numbers above background, TCA Cycle, Oxidative Phosphorylation, Porphyrin Biosynthesis, Ribosome, Polymerases, Proteasome, Cell Cycle, and Cell Adhesion. Gene Ontology (GO) annotation was used for additional validation of gene classification results. A total of 551 GO annotated genes and 468 unannotated genes were classified to the 8 pathways. The primary and secondary classifications of genes revealed known pathway relationships and provide the potential for discovering new pathway relationships.     

Monitoring of protein profiles for the optimization of recombinant fermentation processes using public domain databases

The expression of human superoxide dismutase in fed-batch fermentation of E. coli HMS174(DE3)(pET3ahSOD) was studied as model system. Due to the frequently used strong T7 promoter system a high metabolic load is exerted, which triggers stress response mechanisms and finally leads to the differentiation of the host cell. As a consequence, host cell metabolism is partly shifted from growth to survival accompanied by significant alterations of the protein pattern. In terms of process optimization two-dimensional electrophoresis deserves as a powerful tool to monitor these changes on protein level. For the analysis of samples derived from different states of recombinant protein production wide-range Immobiline Dry Strips pH 3-10 were used. In order to establish an efficient procedure for accelerated process optimization and to avoid costly and time-consuming analysis like mass spectrometry (MS), a database approach for the identification of significant changes of the protein pattern was evaluated. On average, 935 spots per gel were detected, whereby 50 are presumably stress-relevant. Out of these, 24 proteins could be identified by using the SWISS-2DPAGE database (www.expasy.ch/ch2d/). The identified proteins are involved in regulatory networks, energy metabolism, purine and pyrimidine nucleotide synthesis and translation. By this database approach, significant fluctuations of individual proteins in relation to recombinant protein production could be identified. Seven proteins show strong alterations (>100%) directly after induction and can therefore be stated as reliable marker proteins for the assessment of stress response. For distinctive interpretation of this highly specific information, a bioinformatic and statistic tool would be essential in order to perceive the role and contribution of individual proteins in stress response.     

Study of mRNA expression of Arabidopsis thaliana under stimulation using modified differential display RT-PCR with silver staining

We studied differential expressions of Arabidopsis thaliana seedlings under sound stimulation using modified differential display RT-PCR with silver staining in this paper. Six differentially expressed cDNA fragments were obtained. Molecular weight of fragments was between 200 and 600 bp, respectively. On the base of the experimentation, we considered sound stress would have been a positive or negative influence on plant growth. The experimental results indicated some genes was activated, meanwhile some were restrained under after stimulation under sound stress.     

Studies on the Electronic Structures of the C_60, C_60H_60 and C_60F_60

The present paper represents the electronic structures of the cluster C60 and its derivatives C60H60 and C60F60 with FOOT-type of structure. On the basis of the total energies and molecular orbital energies from CNDO/2 calculations the clusters' stabilities, electronic configurations and charge distributions are discussed. The calculation results and discussion are very beneficial to understanding physical and chemical properties of the cluster C60 and its derivatives.     

Broken inter-C60 bonds as the cause of magnetism in polymeric C60: a density functional study using C60 dimers

Bond breaking in C60-C60 dimeric units is believed to play an important role in the onset of magnetism in 2D polymeric C60. On the basis of density-functional theory, the calculations we present here provide further insight into this mechanism through a quantitative characterization of the bond-breaking processes in the isolated dumbbell-shaped C60 dimer. In particular, the analysis of the calculated potential energy surfaces for the low-lying singlet and triplet states identifies and locates the S0-T2 crossing point, which is crucial for the transition to a magnetic state to take place under thermal conditions. These results also suggest a possible new approach to the production of magnetic polymeric C60.     

The DINGO dataset: a comprehensive set of data for the SAMPL challenge

Part of the latest SAMPL challenge was to predict how a small fragment library of 500 commercially available compounds would bind to a protein target. In order to assess the modellers' work, a reasonably comprehensive set of data was collected using a number of techniques. These included surface plasmon resonance, isothermal titration calorimetry, protein crystallization and protein crystallography. Using these techniques we could determine the kinetics of fragment binding, the energy of binding, how this affects the ability of the target to crystallize, and when the fragment did bind, the pose or orientation of binding. Both the final data set and all of the raw images have been made available to the community for scrutiny and further work. This overview sets out to give the parameters of the experiments done and what might be done differently for future studies.     

Multiplexed detection of ions and mRNA expression in single living cells

In order to push forward into new areas of medical and biological research, new techniques must be developed that will enable a complex investigation into cellular processes. This involves investigating not only the different expression levels inside of a cell but also the ability to analyze how those expression levels are connected to one another. In order to accomplish this level of exploration, different types of analytes must be investigated simultaneously inside of single cells, thereby allowing their expression levels to be directly compared. To accomplish this, we have developed a method of detecting and monitoring mRNA expression levels and ion concentrations simultaneously inside of the same single cell. We have utilized this technique in studying the effects of an anti-cancer agent on human breast carcinoma cells. Using this approach, we are able to shed light onto the complex connections between genes and ions inside the cell that is not possible with any other existing technique.     

Investigating the provenance of un-dyed spun cotton fibre using multi-isotope profiles and chemometric analysis

The analysis of un-dyed spun cotton fibres can be challenging within a forensic science context where discrimination of one fibre from another is of importance. Conventional microscopic and chemical analysis of these fibres is generally unsuccessful because of their similar morphology. In this work we have explored the potential of isotope ratio mass spectrometry (IRMS) as a tool for spun cotton fibre analysis in an attempt to reveal any discriminatory information available. Seven different batches of un-dyed spun cotton fibre from four different countries were analysed. A combination of the hydrogen and oxygen isotopic data facilitated the correct association of the samples, demonstrating, for the first time, the applicability of IRMS to fibre analysis in this way.     

Analysis of the phase transitions in alkyl-mica by density and pressure profiles

In a previous work [Heinz, Castelijns, and Suter, J. Am. Chem. Soc. 115, 9500 (2003)], we developed an accurate force field and simulated the phase transitions in C18-mica (octadecyltrimethylammonium-mica) as well as the absence of such transitions in 2C18-mica (dioctadecyldimethylammonium-mica) between room temperature and 100 degrees C. Here we analyze (i) average z coordinates of the carbon atoms and interdigitation of the hydrocarbon bilayers, (ii) density profiles, and (iii) pressure profiles of the structures along all Cartesian axes. In C18-mica, the standard deviation in the z coordinate for the chain atoms is high and more than doubles in the disordered phase. The order-disorder transition is accompanied by a change in the orientation of the ammonium head group, as well as decreasing tensile and shear stress in the disordered phase. In 2C18-mica, the standard deviation in the z coordinate for the chain atoms is low and does not increase remarkably on heating. The backbones display a highly regular structure, which is slightly obscured by rotations in the C18 backbones and minor head group displacements at 100 degrees C. Close contacts between the bulky head groups with sidearms cause significant local pressure which is in part not relieved at 100 degrees C. An increase of the basal-plane spacing at higher temperature is found in both systems due to larger separation between the two hydrocarbon layers and an increased z spacing between adjacent chain atoms (=decreased tilt of the chains relative to the surface normal), and, in C18-mica only, a stronger upward orientation of the C18 chain at the ammonium head group. The likelihood for chain interdigitation between the two hydrocarbon layers is 24%-30% for C18-mica, and 65%-26% for 2C18-mica (for 20-100 degrees C).     

Tuning the Morphology and State of Aggregation of Fullerene C60 using Non-ionic Surfactants

Colloid Journal - The effect of various surfactants on aggregation of fullerene C60 is discussed. Formation of ordered structures via C60-surfactant interactions at a specific [C60]/[Triton X-100]...