Scientific Publications 2006
A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z
N
2006. "Preparation of Ultrafine Chalcopyrite Nanoparticles via the Photochemical Decomposition of Molecular Single-Source Precursors." Nano Letters 6(6):1218-1223. doi:10.1021/nl060661f Abstract The synthesis and characterization of ultrafine CuInS2 nanoparticles are described. Ultraviolet irradiation was used to decompose a molecular single source precursor, yielding organic soluble ~2 nm sized nanoparticles with a narrow size distribution. UV-vis absorption, 1H and 31P{1H} NMR, and fluorescence spectroscopies and mass spectrometry were used to characterize decomposition of the precursors and nanoparticle formation. The nanoparticles were characterized by high-resolution transmission electron microscopy (HRTEM), scanning electron microscopy energy dispersive X-ray spectroscopy, powder X-ray diffraction (XRD), electron diffraction, inductively coupled plasma analysis, UV-vis absorption spectroscopy, and fluorescence spectroscopy. They have a wurzite-type crystal structure with a copper-rich composition. The hypsochromic shift in their emission band due to quantum confinement effects is consistent with the size of the nanocrystals indicated in the HRTEM and XRD analyses.
2006. "First-principles study of Sb adsorption on Ag (110)(2×2)." Chemical Physics 326(2-3):583-588. Abstract The adsorption of antimony atom on the Ag(110) surface has been studied within the density functional theory framework. It was turned out that Sb-Ag surface alloy was formed in which Sb atoms substitute Ag atom in the outermost layer and subsurface site absorption was not preferred, suggesting that Sb is well segregated to the surface. Geometric analysis showed that rumpling between substitutional Sb and Ag in the alloy surface is negligible. These results are found to agree well with the experimental finding of Nascimento et al. [Surf. Sci. 572 (2004) 337]. In addition, investigation of the diffusion of Ag atom on bare and Sb-covered Ag(110) surface showed that Ag adatoms will jump along the so call in-channel direction and Sb substitution has little effect on the diffusion of Ag adatoms on Ag(110) surface. Such diffusion behavior was found to be different from that of Ag adatoms on Ag(111) surface, where the diffusion energy barrier was reported to be significantly increased upon Sb substitution [Phys. Rev. Lett. 73 (1993) 2437].
2006. "Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: A quantitative analysis." Genetics 174(4):2229-2243. doi:10.1534/genetics.106.065862 Abstract The modest correlation between mRNA expression and protein abundance in large scale datasets is explained in part by experimental challenges, such as technological limitations, and in part by fundamental biological factors in the transcription and translation processes. Among various factors affecting the mRNA-protein correlation, the roles of biological factors related to translation are poorly understood. In this study, using experimental mRNA expression and protein abundance data collected from Desulfovibrio vulgaris by DNA microarray and LC-MS/MS proteomic analysis, we quantitatively examined the effects of several translational-efficiency-related sequence features on mRNA-protein correlation. Three classes of sequence features were investigated according to different translational stages: i) initiation: Shine-Dalgarno sequences, start codon identity and start codon context; ii) elongation: codon usage and amino acid usage; and iii) termination: stop codon identity and stop codon context. Surprisingly, although it is widely accepted that translation initiation is a rate-limiting step for translation, our results showed that the mRNA-protein correlation was affected the most by the features at elongation stages, codon usage and amino acid composition (7.4-12.6% and 5.3-9.3% of the total variation of mRNA-protein correlation, respectively), followed by stop codon context and the Shine-Dalgarno sequence (2.5-4.2% and 2.3%, respectively). Taken together, all sequence features contributed to 18.4-21.8% of the total variation of mRNAprotein correlation. As the first comprehensive quantitative analysis of the mRNA-protein correlation in bacterial D. vulgaris, our results suggest that the traditional view of the relative importance of various sequence features in prokaryotic protein translation might be questionable.
2006. "Integrated analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: Zero-Inflated Poisson regression models to predict abundance of undetected proteins." Bioinformatics 22(13):1641-1647. doi:10.1093/bioinformatics/btl134 Abstract Abstract Advances in DNA microarray and proteomics technologies have enabled high-throughput measurement of mRNA expression and protein abundance. Parallel profiling of mRNA and protein on a global scale and integrative analysis of these two data types could provide additional insight into the metabolic mechanisms underlying complex biological systems. However, because protein abundance and mRNA expression are affected by many cellular and physical processes, there have been conflicting results on the correlation of these two measurements. In addition, as current proteomic methods can detect only a small fraction of proteins present in cells, no correlation study of these two data types has been done thus far at the whole-genome level. In this study, we describe a novel data-driven statistical model to integrate whole-genome microarray and proteomic data collected from Desulfovibrio vulgaris grown under three different conditions. Based on the Poisson distribution pattern of proteomic data and the fact that a large number of proteins were undetected (excess zeros), Zero-inflated Poisson models were used to define the correlation pattern of mRNA and protein abundance. The models assumed that there is a probability mass at zero representing some of the undetected proteins because of technical limitations. The models thus use abundance measurements of transcripts and proteins experimentally detected as input to generate predictions of protein abundances as output for all genes in the genome. We demonstrated the statistical models by comparatively analyzing D. vulgaris grown on lactate-based versus formate-based media. The increased expressions of Ech hydrogenase and alcohol dehydrogenase (Adh)-periplasmic Fe-only hydrogenase (Hyd) pathway for ATP synthesis were predicted for D. vulgaris grown on formate.
2006. "Multispectral/hyperspectral image enhancement for biological cell analysis." Cytometry. Part A 69(8):897-903. doi:10.1002/cyto.a.20294 Abstract The paper shows new techniques for analyzing cell images taken with a microscope using multiple filters to form a datacube of spectral image planes. Because of the many neighboring spectral samples, much of the datacube appears as redundant, similar tissue. The analysis is based on the nonGaussian statistics of the image data, allowing for remapping of the data into image components that are dissimilar, and hence isolate subtle, spatial object regions of interest in the tissues. This individual component image set can be recombined into a single RGB color image useful in real-time location of regions of interest. The algorithms are susceptible to parallelization using Field Programmable Gate Array hardware processing.
